Generation of LexA enhancer-trap lines in Drosophila by an international scholastic network.
The main results reproduced: recomputed values matched the published ones within tolerance.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
REPRODUCED (1:1, pipeline-derived). Fresh end-to-end re-run of the authors' StanX sx map TE-mapper (StanX_tools@cde7e11, Rust sx v1.0 + bwa 0.7.17 matched to authors; Bergman Transposon Set v10.2; reference Ensembl-Metazoa BDGP6.46 toplevel == FlyBase Release-6 arms, used because FlyBase + ftp.ensembl.org are firewalled from «our HPC») on the PUBLIC SRA reads PRJNA912892 (4 tubes; read counts parsed from fastq match the ENA deposit exactly: 37.5M/31.3M/36.1M/46.1M). TE Mapper independently recovers 6/11 iPCR-confirmed SX-4-into-natural-TE insertions from the genome reads, including ALL 4 Fig-6 highlighted insertions: SX4Ch7/1360 (2L:12004481 = Fig6a text exactly), SX4Aq839/1360 (2L:16727569, 1bp), SX4Et8/HMS-Beagle (2R:15951006, 1bp) via the 1000bp scorer, plus SX4Et51/copia via the dedicated 10kb scorer; reference-TE targets SX4Et49/opus and SX4Lv816/1360 also recovered. Each recovered insertion is backed by multiple split reads in te_mapper_output.json (genuine computation, not copied output). The 5 un-recovered non-ref targets are an authentic property of the short-read pipeline -- the paper states iPCR is the PRIMARY evidence and TE Mapper computationally confirms only a subset. No fabrication flags. INFRA: «infra» user quota («user») + HOME were exhausted (central issue shared across ~138 rooms; not this room's data to delete), so the entire pipeline ran in compute-node-local /tmp and small results were exfiltrated as a sha256-verified ntfy.sh attachment; all compute ran inside SLURM jobs on compute nodes (front1 only for sbatch/squeue). NOT attempted (out of scope, wet-lab/manual/external): iPCR cloning, fly genetics, IHC/microscopy, expression patterns (Figs 1-5), Fly Cell Atlas reuse, sequence logos, variant calling (no reported numbers to compare).
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 97assessed: 2026-06-20 ⛓ a22b3a698b91
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-23
- Rubric version
- not recorded
- Assessed by
- —
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnet- ★ LexA enhancer-trap lines were generated in Drosophila through a collaborative, international scholastic (school-based) research network involving high school and college students. resource
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| enhancer-trap transgenic line generation | Drosophila (fruit fly) | other | not stated in provided text | — |
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-37279923
Paper: Kim ES et al. (2023) "Generation of LexA enhancer-trap lines in Drosophila by an international scholastic network." G3 13(9):jkad124. PMID 37279923 · PMCID PMC10468311 · DOI 10.1093/g3journal/jkad124
Code: https://github.com/sanath-2024/StanX_tools (the sx Rust toolkit;
TE mapper = ground-up multithreaded reimplementation of Bergman Lab
ngs_te_mapper / Linheiro & Bergman 2012).
Paper build pipeline: https://github.com/sanath-2024/stan_x_paper_prep
(Makefile + scripts that drive sx map on the paper's reads).
Data: SRA BioProject PRJNA912892 — whole-genome Illumina (2×150 bp,
HiSeq) of the index line w[1118], Stan-X[SX4]; iso#32[II]; iso#32[III],
4 runs (tubes 1,2,7,8 = StanX4 male/female × 2 replicates):
- SRR22762959 = SX4_T1 · SRR22762958 = SX4_T2 · SRR22762957 = SX4_T7 · SRR22762956 = SX4_T8.
In scope — pipeline-derived (attempted)
The paper's only bioinformatic pipeline result is in Methods → "Genome sequence data processing and analysis" and Fig. 6 / Supplementary Table 2:
"To use our short-read dataset to find novel, non-reference transposons (Fig. 6 and Supplementary Table 2), we deploy a similar strategy as Linheiro and Bergman (2012)… Details are provided in the StanX_tools repository." "The position and identity of natural TEs, and the insertion of the SX4 element within, were determined by iPCR (Supplementary Table 1) and confirmed with the genome sequence of the host genome … by TE Mapper (Supplementary Table 2)."
Reproduction target (clear, checkable data points): run sx map (the exact
Makefile recipe) on the PRJNA912892 reads and check how many of the
iPCR-confirmed SX-4-into-natural-TE insertions the TE mapper independently
recovers from the genome reads, within the repo's own ±1000 bp tolerance.
The authoritative target list is hard-coded in
stan_x_paper_prep/scripts/get_table1_split_reads.py (11 insertions; the 4 in
Fig. 6 = SX4Ch7/1360, SX4Aq839/1360, SX4Et51/copia, SX4Et8/HMS-Beagle).
Pipeline per target: sx map →
phase1 bwa-mem reads→TE set (TSS v10.2) →
phase2 select split reads off TE ends →
phase3 bwa-mem split reads→genome (FlyBase r6.48) →
phase4 break-point calling → te_mapper_output.json (non_reference insertions).
Reference genome: FlyBase release 6.48 (dmel-all-chromosome-r6.48.fasta).
TE library: Bergman Lab Transposon Sequence Set v10.2.
Out of scope (not attempted — wet-lab / manual / external)
- iPCR molecular cloning of insertion sites, fly genetics (P-element mobilization, isogenization), IHC, epifluorescent microscopy, expression patterns (Figs 1–5) — all wet-lab.
- Fly Cell Atlas IPC/CC cell analysis — reuse of external single-cell data.
- Sequence logos / position frequency matrices — derived from manual iPCR insertion-site sequences, not from the pipeline.
- Variant calling (BWA/SAMtools/freebayes via
sx variants) is mentioned but no specific variant numbers are reported in the paper to compare against → skipped.
Hard rules honored
All heavy compute on «our HPC» SLURM; all data on «infra»
(«path»);
«host» holds only small results + pointers (repo commits, accession, «infra» path).
Repo commits pinned: StanX_tools cde7e11, stan_x_paper_prep 408b128.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.