140/150 Galaxy passes versus 138/150 Open-ended code passes.
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
5 model configurations, two execution conditions
Each score covers the same 50 verified items with three independent replicates. Every model and execution condition is reported separately. Superseded configurations stay published for reference and are labelled as such.
1500 runs50 items3 replicates
May 2026 · historical baseline
Galaxy-API code without UDTs
42/50tasks correct · 84.0%
UDTs were not available in this campaign. All 50 runs used ordinary, noninteractive Galaxy tools; no user-defined tool could be created or run.
The retained records include a review note, prompt, answer evidence, run trace, and Galaxy history evidence for every task. This establishes that at least 42 of these 50 tasks can be solved without a UDT; it does not show that the other eight require one.
Jul 14, 2026
Codex GPT-5.5
Galaxy-API code
93.3%
140/150 correct
UDT usage
66.7%
100/150 replicates
69 UDT-only · 31 UDT + standard tools
replicate 192.0%46/50replicate 294.0%47/50replicate 394.0%47/50
Open-ended code
92.0%
138/150 correct
replicate 192.0%46/50replicate 292.0%46/50replicate 392.0%46/50
Jul 31-Aug 3, 2026
Codex GPT-5.6 Sol
Galaxy-API code
92.7%
139/150 correct
UDT usage
34.7%
52/150 replicates
31 UDT-only · 21 UDT + standard tools
replicate 192.0%46/50replicate 294.0%47/50replicate 392.0%46/50
Open-ended code
89.3%
134/150 correct
replicate 186.0%43/50replicate 292.0%46/50replicate 390.0%45/50
Jul 31-Aug 3, 2026
Codex GPT-5.6 Luna
Galaxy-API code
88.7%
133/150 correct
UDT usage
39.3%
59/150 replicates
17 UDT-only · 42 UDT + standard tools
replicate 194.0%47/50replicate 286.0%43/50replicate 386.0%43/50
Open-ended code
89.3%
134/150 correct
replicate 190.0%45/50replicate 292.0%46/50replicate 386.0%43/50
Aug 15-Oct 23, 2026
DeepSeek V4 Pro via Codex
Galaxy-API code
83.3%
125/150 correct
UDT usage
15.3%
23/150 replicates
7 UDT-only · 16 UDT + standard tools
replicate 182.0%41/50replicate 284.0%42/50replicate 384.0%42/50
Open-ended code
82.7%
124/150 correct
replicate 182.0%41/50replicate 282.0%41/50replicate 384.0%42/50
Jul 16, 2026
DeepSeek V4 Pro via Claude Code Superseded
Preview build of DeepSeek V4 Pro, run through Claude Code. Superseded by the released model run through Codex on Aug 15-17, 2026.
Galaxy-API code
84.0%
126/150 correct · 1/150 invalid
UDT usage
35.3%
53/150 replicates
18 UDT-only · 35 UDT + standard tools
replicate 184.0%42/50replicate 280.0%40/50replicate 388.0%44/50
Open-ended code
72.7%
109/150 correct
replicate 172.0%36/50replicate 270.0%35/50replicate 376.0%38/50
Galaxy versus Open-ended code
Pass-count differences within each model configuration.
139/150 Galaxy passes versus 134/150 Open-ended code passes.
133/150 Galaxy passes versus 134/150 Open-ended code passes.
125/150 Galaxy passes versus 124/150 Open-ended code passes.
126/150 Galaxy passes versus 109/150 Open-ended code passes.
Item-by-item results
Replicate markers show pass or fail. Open an item for all answers, workflows, usage, traces, and Galaxy histories.
50 items
Scroll horizontally to compare all 10 result columns.
| Item | Question | Codex GPT-5.5 | Sol | Luna | DeepSeek V4 Pro | DeepSeek previewsuperseded | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Galaxy | Open-ended code | Galaxy | Open-ended code | Galaxy | Open-ended code | Galaxy | Open-ended code | Galaxy | Open-ended code | ||
| bix-6-q4general | What is the Spearman correlation coefficient between the replicate MAGeCK P-values for chronic round 1? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-11-q1phylogenetics | What is the difference between median treeness values for fungi versus animals? Report the difference as a decimal proportion (not percentage). | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-11-q2phylogenetics | What percentage of fungal genes have treeness values above 0.06? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-12-q2phylogenetics | What is the median percentage of parsimony informative sites across fungal gene alignments? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-12-q4phylogenetics | What is the Mann-Whitney U statistic when comparing parsimony informative site percentages between animals and fungi? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 |
| bix-12-q5phylogenetics | What is the maximum number of parsimony informative sites in any animal gene alignment? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-12-q6phylogenetics | What is the Mann-Whitney U statistic when comparing raw parsimony informative site counts between animals and fungi? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-14-q1variant callset | In the BLM mutation carrier cohort, what fraction of coding variants with a variant allele frequency (VAF) below 0.3 are annotated as synonymous? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-16-q1crispr dependency | In the provided data, what gene symbol has the strongest negative Spearman correlation between its expression and essentiality? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-16-q3crispr dependency | How many genes in the provided data show strong positive Spearman correlation between expression and essentiality across cell lines, with a correlation coefficient >= 0.6? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-16-q4crispr dependency | Using a Spearman Rank correlation test and Benjamini-Hochberg multi-test correction, what percentage of genes show a statistically significant correlation between expression and essentiality, in either direction? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 |
| bix-17-q2variant callset | Among patients classified as BLM mutation carriers, what is the median number of somatic CHIP variants - defined as variants with a Variant Allele Frequency (VAF) < 0.3? Prior to analysis, exclude all variants that are Intronic, Intergenic, in UTR regions, or have Reference zygosity. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-18-q1general | In a P. aeruginosa swarming analysis, what is the mean circularity measurement for the genotype showing the largest mean area? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-18-q3general | What is the approximate percent reduction in mean colony area for the ΔlasR mutant compared to wildtype? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-20-q3variant callset | Among samples with a 'Carrier' BLM mutation status, what proportion of somatic CHIP variants (VAF < 0.3) with ClinVar classifications are classified as Benign or Likely Benign? The proportion of somatic CHIP variants should be calculated after filtering out intronic, intergenic, UTR regions, and reference (non-variant) calls. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-22-q1general | After calculating Pearson correlations between gene length and average gene expression levels for protein-coding genes, in which immune cell type (CD4, CD8, CD14, or CD19) is the correlation the weakest (lowest absolute correlation value)? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-22-q4general | What is the Pearson correlation coefficient between gene length and mean expression (across samples) for expressed protein-coding genes (total counts ≥ 10) in CD14 immune cells? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-24-q2transcriptomics | Using differential expression analysis (padj < 0.05, |log2FC| > 0.5) and GO Biological Process enrichment analysis, determine whether upregulation or downregulation of genes primarily drives the metabolic effects of CBD treatment in CRC cells. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-26-q3transcriptomics | Among significantly upregulated genes in the iron-depleted glucose condition (FeMinus), how many genes contribute to the enrichment of the 'ABC transporters' term after conducting KEGG pathway enrichment analysis? Use an absolute log2 fold change cut off 1.5 and an adjusted p-value threshold of 0.05. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-26-q5transcriptomics | In P. aeruginosa KEGG pathway enrichment analysis, how many pathways are significantly enriched under iron-depleted conditions but show no significant enrichment under innate media conditions? Perform KEGG pathway enrichment analysis using genes with |log2FoldChange| > 1.5 and adjusted p-value < 0.05. Consider pathways significantly enriched if their enrichment adjusted p-value < 0.05. | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-27-q5expression matrix pca | After performing principal component analysis (PCA) with 100 components on the log10-transformed gene expression matrix (with pseudocount of 1, samples as rows and genes as columns), what percentage of the total variance in the dataset is explained by the first principal component (reported as a percentage between 0 and 100)? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-28-q3phylogenetics | Using PhyKIT to calculate long branch scores, what is the median long branch score for the fungal gene 996662at2759? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-30-q3transcriptomics | What is the ratio of significant (p <= 0.05) differentially expressed miRNAs between patient and control groups identified following Bonferroni correction compared to Benjamini-Yekutieli correction? Provide your answer as a ratio in the format "Bonferroni:Benjamini-Yekutieli". | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 |
| bix-31-q2transcriptomics | Using the batch-corrected read counts with batch as a covariate in the design formula, perform a sex-specific (M vs F) differential expression analysis (abs lfc>0.5, basemean>10 and using lfc shrinkage), what is the log2 fold change of FAM138A? Use pydeseq2 with default shrinkage method. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 |
| bix-32-q2transcriptomics | Using KEGG over-representation analysis (ORA), how many pathways are significantly enriched (absolute value of lfc > 1.5) in the same direction for all three mutant strains (97, 98, and 99), relative to wildtype? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 |
| bix-34-q2phylogenetics | What is the median patristic distance for the fungal gene 981902at2759? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-34-q5phylogenetics | What is the ratio of median mean patristic distances between fungi and animals? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 |
| bix-35-q1phylogenetics | Calculate the evolutionary rate for the BUSCO gene 156083at2759 using PhyKIT's evoluionary_rate function. What is the gene's evolutionary rate in animals? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-35-q2phylogenetics | What is the Mann-Whitney U statistic value for the comparison of evolutionary rates between animals and fungi across all genes? Use PhyKIT's evo_rate function to calculate evolutionary rates. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-37-q1general | Based on the proteomics data, what is the fold change in ENO1 protein abundance between tumor and normal samples? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-37-q4general | What is the log2 fold change value (rounded to 2 decimal places) for ENO1 when comparing tumor samples to normal samples in the proteomics dataset? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-38-q1phylogenetics | What is the fold-change in median tree length between fungi and animals after calculating tree lengths with PhyKIT? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-41-q5general | In a bacterial swarming assay compared mixed cultures of Strain 287 and Strain 98 at various ratios, which ratio produced colonies with a mean area and circularity value that is most similar to the mean area and circularity values observed in Strain 1? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-43-q2transcriptomics | What is the odds ratio for p53-mediated cell cycle gene regulation in an enrichment analysis using gseapy with Reactome_2022 using all statistically differentially expressed genes from a pydeseq2 analysis that includes all related treatment groups (DMSO, DMSO_Serum_starvation, Cisplatin_IC50_CBD_IC50, Cisplatin_IC50_CBD_IC50_Serum_starvation_16h) for proper dispersion estimation, after pre-filtering to keep only genes with counts greater than 10 in at least one of all 30 samples, (padj<=0.05, absolute lfc>=0.5, baseMean>=10) between CBD/cisplatin combination treatment and DMSO? | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 |
| bix-43-q4transcriptomics | After performing differential gene expression analysis comparing CBD/cisplatin treatment vs DMSO control (using padj < 0.05 and |log2FC| ≥ 0.5), followed by enrichment analysis using gseapy with Reactome_2022 gene sets, what is the overlap ratio (DEGs found in pathway / total pathway genes) for the 'TP53 Regulates Transcription Of Cell Cycle Genes' pathway in the enrichment results? Express your answer as a fraction (e.g., X/Y). | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-45-q1phylogenetics | What is the p-value from a Mann-Whitney U test comparing RCV scores between animal and fungal orthologs using PhyKIT's rcv function? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-46-q4transcriptomics | What is the log2 fold change value rounded to 2 decimal points for the phenazine pathway gene PA14_35160 in the ΔrhlI mutant? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-47-q3variant callset | Which gene has the most non-reference variants in the oldest male carrier? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-49-q4transcriptomics | What is the total number of significantly differentially expressed genes (padj < 0.05) when performing DESeq2 differential gene expression analysis with apeglm LFC shrinkage, comparing ASXL1 mutation (disease) vs control, while controlling for sex as a covariate? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 |
| bix-51-q2model fitting | What is the Akaike Information Criterion (AIC) for the logistic regression model that uses BMI as the sole predictor of treatment response (efficacy PR)? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-51-q8model fitting | In a simple logistic regression model assessing age and camrelizumab treatment response, what is the coefficient estimate (change in log-odds) for age? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-52-q2general | What is the mean of per-chromosome densities (CpGs per base pair) for filtered (>90% or <10% methylation) unique age-related CpGs across all chromosomes (only including those with at least one filtered CpG) in the Jackdaw genome? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-52-q6general | Which chromosome in the Jackdaw genome shows the highest density of age-related CpG sites? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-52-q7general | How many individual methylation measurements (rows) are removed when filtering out measurements that do not show >90% or <10% methylation in the Zebra Finch dataset? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 |
| bix-53-q2transcriptomics | Perform differential expression analysis on the RNA-seq dataset (KL1-3 vs WL1-3) using criteria p < 0.05, |log2FC| > 1, baseMean > 10 with LFC shrinkage. Then repeat the analysis excluding the third replicates (KL3, WL3) due to batch effects and describe how this affects the number of significantly differentially expressed genes, indicating the direction of change (increase, decrease, or no change). | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-53-q5transcriptomics | Using the gseapy package and WikiPathways_2019_Mouse as a reference library, what is the fraction of oxidative stress-related pathways (pathway name contains "oxidative") among the top 20 enriched pathways based on all significantly differentially expressed genes (p<0.05, absolute lfc>1, baseMean>10 and following lfc shrinkage)? Round to 1 decimal place. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-54-q7model fitting | What is the maximum colony area predicted at the optimal frequency (proportion of strain 287 in the mixtures) according to the best-fitting model among quadratic, cubic and natural spline (df=4) models? Use R for model fitting. | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 1/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 |
| bix-55-q1general | How many single-copy orthologs are complete and present in all four proteomes after BUSCO analysis with the eukaryota_odb10 lineage? | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 |
| bix-61-q2general | What is the average coverage depth across the entire reference genome for the MDR sample (SRR35233585) rounded to 4 decimal places? Map the trimmed reads with BWA-MEM (read group @RG\tID:SRR35233585\tSM:SRR35233585\tPL:ILLUMINA\tLB:lib1\tPU:unit1) and use samtools for depth calculations. | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 | 2/3 replicate 1 replicate 2 replicate 3 | 3/3 replicate 1 replicate 2 replicate 3 |
| bix-61-q5variant callset | What is the Ts/Tv ratio for the MDR sample (SRR35233585) rounded to 2 decimal places? | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 | 0/3 replicate 1 replicate 2 replicate 3 · invalid | 0/3 replicate 1 replicate 2 replicate 3 |
Legacy result set
Jul 6 Codex four-condition experiment
The previous skills/no-skills comparison and its 50 item pages are preserved as a separate archive.