CompBioBench evaluation results
Completed evaluation replicates are shown here. Official leaderboard scores correspond to the displayed answer sets; scores awaiting submission or evaluation are left blank.
100 items5 models25 replicates
July-August 2026
Codex GPT-5.5
6 replicates
Galaxy
85.7%
official leaderboard mean across 3 replicates
UDT usage
89.3%
268/300 question runs
164 UDT-only · 104 UDT + standard tools
31 standard tools only
1 with no analysis tools recorded
Replicate 184%official leaderboardReplicate 287%official leaderboardReplicate 386%official leaderboard
Anycode
86.3%
official leaderboard mean across 3 replicates
Replicate 187%official leaderboardReplicate 288%official leaderboardReplicate 384%official leaderboard
August 2026
Codex GPT-5.6 Sol
6 replicates
Galaxy
92.3%
official leaderboard mean across 3 replicates
UDT usage
79.7%
239/300 question runs
121 UDT-only · 118 UDT + standard tools
61 standard tools only
Replicate 193%official leaderboardReplicate 291%official leaderboardReplicate 393%official leaderboard
Anycode
91.0%
official leaderboard mean across 3 replicates
Replicate 188%official leaderboardReplicate 290%official leaderboardReplicate 395%official leaderboard
August 2026
Codex + DeepSeek-v4-pro-0813
6 replicates
Galaxy
85.3%
official leaderboard mean across 3 replicates
UDT usage
51.0%
153/300 question runs
48 UDT-only · 105 UDT + standard tools
146 standard tools only
1 with no analysis tools recorded
Replicate 186%official leaderboardReplicate 285%official leaderboardReplicate 385%official leaderboard
Anycode
85.0%
official leaderboard mean across 3 replicates
Replicate 181%official leaderboardReplicate 286%official leaderboardReplicate 388%official leaderboard
August 2026
Codex GPT-5.6 Luna
6 replicates
Galaxy
84.7%
official leaderboard mean across 3 replicates
UDT usage
61.3%
184/300 question runs
61 UDT-only · 123 UDT + standard tools
114 standard tools only
2 with no analysis tools recorded
Replicate 186%official leaderboardReplicate 283%official leaderboardReplicate 385%official leaderboard
Anycode
84.7%
official leaderboard mean across 3 replicates
Replicate 185%official leaderboardReplicate 285%official leaderboardReplicate 384%official leaderboard
September 2026
Codex GPT-6 Astra
1 replicate
Anycode
93.0%
official leaderboard; 1 replicate
Replicate 193%official leaderboard
Token usage
Total reported model tokens for each published 100-item replicate.
| Model | Execution | Replicate 1 | Replicate 2 | Replicate 3 | Median |
|---|---|---|---|---|---|
| Codex GPT-5.5 | Galaxy | 150.4M100/100 items | 253.7M100/100 items | 364.9M99/100 items | 253.7M |
| Codex GPT-5.5 | Open-ended code | 132.1M100/100 items | 156.4M100/100 items | 134.1M100/100 items | 134.1M |
| Codex GPT-5.6 Sol | Galaxy | 828.4M100/100 items | 791.2M100/100 items | 1.11B100/100 items | 828.4M |
| Codex GPT-5.6 Sol | Open-ended code | 235.2M100/100 items | 216.3M100/100 items | 277.7M100/100 items | 235.2M |
| Codex + DeepSeek-v4-pro-0813 | Galaxy | 1.18B100/100 items | 1.35B100/100 items | 1.66B100/100 items | 1.35B |
| Codex + DeepSeek-v4-pro-0813 | Open-ended code | 749.0M100/100 items | 700.4M100/100 items | 707.7M100/100 items | 707.7M |
| Codex GPT-5.6 Luna | Open-ended code | 591.2M100/100 items | 688.3M100/100 items | 628.1M100/100 items | 628.1M |
| Codex GPT-5.6 Luna | Galaxy | 1.92B100/100 items | 1.48B100/100 items | 1.83B100/100 items | 1.83B |
| Codex GPT-6 Astra | Open-ended code | 112.9M100/100 items | Not run | Not run | 112.9M |
Totals count the selected run for each question, including adopted reruns, rather than adding superseded attempts. Input includes cached input; total tokens are input plus output. Token usage is missing for one item in 1 replicate.
Item-by-item results
Markers show answer availability. Open any item for every recorded answer, workflow, usage record, and available Galaxy history.
100 items
Scroll horizontally to compare all 9 result columns.
| Item | Question | GPT-5.5 | Sol | DeepSeek-v4-pro-0813 | Luna | Astra | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Galaxy | Anycode | Galaxy | Anycode | Galaxy | Anycode | Galaxy | Anycode | Anycode | ||
| ensembl-grab-q1Genomics | Convert all of the following to Ensembl gene IDs. Provide the ID without the Ensembl version (e.g., ENSGXXXXXXXXXXXX not ENSGXXXXXXXXXXXX.XX). Respond with semi-colon separated values, no spaces. Inputs: 1. NM_001276266... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| bam-infer-read-length-q1Genomics | For the given BAM file mt.sorted.bam, infer if it's paired or single ended reads and the read length. Expected output format: 1x57 | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| differential-composition-q1Single-cell | differential.composition.q1.1.mtx.gz and differential.composition.q1.2.mtx.gz contain raw scRNA counts matrices derived from retinal samples of two individuals (one per file, each column is a unique barcode that passes... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| genomic-state-q1Epigenomics | Consider chr11:124,738,681-124,738,772 (hg38). What is the likely purpose of this region? Choose only one. A. Active enhancer, Liver B. Active enhancer, Brain frontal lobe C. Active enhancer, ESC D. Active transcription... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| cryptic-exon-q1Transcriptomics | I have a bulk human RNA-seq fastq file cryptic.exon.q1.fq.gz. There is exactly one highly expressed coding gene that has a cryptic exon in it formed by two novel junctions. Report the HGNC gene symbol (uppercase) for th... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| read-paper-download-file-parse-q1Epigenomics | Take a look at the pdf here: https://www.biorxiv.org/content/10.1101/2023.10.04.560808v2.full.pdf, can you find the exact number of peaks in the COC/L1 cluster? Follow any external links in the paper if additional data... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| huggingface-entropy-q1Machine Learning | Run the DNA language model here: https://huggingface.co/kuleshov-group/caduceus-ph_seqlen-131k_d_model-256_n_layer-16 on the 1000 bp long DNA sequence at hg38 chr12:7792299-7793299. Specifically, mask each base one at a... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| ml-model-track-overlap-q1Epigenomics | Borzoi (Linder et al., doi:10.1038/s41588-024-02053-6) and Sei (Chen et al., doi:10.1038/s41588-022-01102-2) are both DNA sequence models trained to predict genomic assay outputs. Out of the Sei tracks that are linked t... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| compute-gc-content-interval-q1Genomics | Using the GRCh38.p13 human reference genome, retrieve the reference DNA sequence for chromosome 1 from positions 1,000,000 to 1,000,100 (1-based, inclusive) on the '+' strand, and calculate: (1) gc_percent (rounded to 2... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| reverse-search-gwas-q1Population Genetics | Identify the PubMed ID of the study from which this summary statistics in reverse.search.gwas.q1.tsv.gz are derived. Print only the PMID, e.g. 31510655. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| pathogenic-variant-lookup-q1Genomics | Using the human SHH MANE Select transcript on hg38, consider the coding sequence within exon 1. Within this interval, identify all OMIM allelic variants with phenotypes that map to single-nucleotide missense substitutio... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| identify-donor-q1Population Genetics | The pair end fastqs (identify.donor.R1.fq.gz, identify.donor.R2.fq.gz) correspond to reads from one of the 1000G donors (2504 high coverage set) from a 5Mb region of the genome. Identify the donor and report the 1000G s... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| contaminated-rna-q3Transcriptomics | You are given a single-end RNA-seq FASTQ file (contaminated.rna.q3.fq.gz). The sample is expected to be human, but it may contain reads from another organism. Determine the genus of the most likely non-human organism pr... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| hic-differential-loop-q1Epigenomics | Consider the MicroC data for H1 and HFF cells from the following paper: https://doi.org/10.1016/j.molcel.2020.03.003. In the sub-compartment containing the NANOG gene (chr12:7629950-7809597), there is a differential loo... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| encode-atac-pipeline-q1Epigenomics | encode.atac.pipeline.q1.R1.fq.gz and encode.atac.pipeline.q1.R2.fq.gz are paired-end ATAC-seq reads from a human sample. Process them through the ENCODE ATAC-seq pipeline v2.2.3 (https://github.com/ENCODE-DCC/atac-seq-p... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| pooled-infer-donors-q1Single-cell | pooled.infer.donors.q1.bam is an aligned scRNA-seq BAM from a pooled human sample. The file includes cell barcode tags. Determine the number of distinct donors contributing cells to the pool. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| overexpress-tf-q1Epigenomics | We perturbed a primary cell culture with a cocktail of transcription factors (TFs). ATAC-seq is performed on the initial sample and 48 hours after perturbation. overexpress.tf.q1.ref.bed.gz and overexpress.tf.q1.perturb... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| conservation-lookup-q1Genomics | Using the human SHH MANE Select transcript, take the cDNA sequence from the annotated start codon through the end of exon 1. For each of the following species: Pan troglodytes, Macaca mulatta, Pan paniscus, Indri indri,... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| splice-pred-q1Machine Learning | Extract the human genomic DNA sequence from hg38 at chr12:120,196,699-120,201,111. This locus is on the minus strand. Run OpenSpliceAI (v0.0.5) to predict with the OSAIMANE-10000nt models, averaging predictions across a... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| borzoi-rnaseq-q1Machine Learning | Use the Borzoi model (replicate 0) to predict the total RNA-seq coverage on the forward strand for the experiment ENCFF281BWX, over the genomic interval chr1:70157360-70353968 in the hg38 genome. Return the total predic... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| calculate-average-gene-expression-q1Single-cell | Using the single-cell dataset in AnnData format located at pbmc3k.h5ad, determine the average log-normalized expression for the gene S100B in all cells belonging to the group labeled 'B cells' in the 'louvain' metadata... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| covid-patient-q1Single-cell | covid.patients.q1.h5ad contains PBMC scRNA-seq data from 33 donors, who are a mix of healthy and COVID patients. However, the patient metadata is missing. Identify which donors are healthy and which have COVID based on... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| saluki-setup-optimize-q1Machine Learning | Set up the Saluki model detailed in https://doi.org/10.1186/s13059-022-02811-x and use it to optimize the 3' UTR of the mRNA sequence GCCGCCACCATGGTGAGCAAGGGCGAGTAGTGTACATAATAAGGACT. Specifically, perform 3 rounds of di... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| identify-related-q1Population Genetics | You are given identify.related.q1.tfam and identify.related.q1.tped.gz files of genotypes. I need to know if there are any 1st-degree relatives. Print a comma separated, sorted list of all individuals with a 1st-degree... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| ep-interactions-q1Epigenomics | You are given two complementary datasets describing eight candidate distal regulatory element–promoter interactions (EP1–EP8): (1) a Hi-C–like chromatin contact dataset measuring 3D proximity between each element–promot... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| sample-swap-rna-q1Single-cell | I have a scRNA-seq pseudobulk lying around from amphioxus tissue (sample.swap.rna.q1.tsv.gz). I'm not sure, but I suspect there is a sample swap. Can you check if that is the case? If there isn't, respond "None". Else r... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gene-fusion-q2Transcriptomics | You are given a bulk RNA sequencing FASTQ file (gene.fusion.q2.fq.gz) from human. The data contains a synthetic gene that is a fusion of multiple genes. Your task is to identify the genes whose exons make up the fusion... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| retina-score-snps-q1Machine Learning | https://zenodo.org/records/6330053 contains TensorFlow 2 models that are used for scoring the impact of SNPs on ATAC-seq in various cells types, as illustrated in the ScoreSNPs.ipynb notebook in https://zenodo.org/recor... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| atac-tn5-shift-q1Epigenomics | I got a scATAC-seq fragment file (unknown.shift.frag.bed.gz) from a colleague who aligned it to the hg38 genome. However, they applied a non-standard shift to the reads instead of the typical +4/-5. Can you help figure... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| finding-geo-q1Single-cell | finding.geo.q1.h5ad contains a scRNA-seq dataset that is derived from a Supplementary file on GEO, and processed to filter out barcodes with low counts. Find the GSE ID of the corresponding record. Return the GSE ID at... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| deg-simple-q1Transcriptomics | I have bulk RNA-seq fastq files from 2 human samples (deg.simple.q1.sampleA.fq.gz, deg.simple.q1.sampleB.fq.gz). There is exactly one gene that is strongly differentially expressed between the two samples. Report the HG... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| bigwig-density-q1Epigenomics | From the given ENCFF822FDB.bigWig file corresponding to an ENCODE DNase-seq experiment in mouse brain (mm10), find the 1Mbp interval with the 3rd highest total signal intensity. Consider only those intervals that start... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gtf-5-utr-median-len-q1Transcriptomics | From the given GTF MANE.GRCh38.v1.3.refseq_genomic.gtf.gz, report the median 5' UTR, CDS, and 3' UTR lengths (use numpy median function, rounded down to nearest integer). Only consider MANE Select transcripts and those... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| contaminated-rna-q2Transcriptomics | You are given a single end RNA-seq fastq file (contaminated.rna.q2.fq.gz). This file contains mostly human reads and a small fraction of contaminant reads. Identify the contaminant species present. Report the answer as... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| sample-swap-rna-q2Single-cell | I have a scRNA-seq pseudobulk lying around from wheat (sample.swap.rna.q2.tsv.gz). I'm not sure, but I suspect there is a sample swap. Can you check if that is the case? If there isn't, respond "None". Else respond with... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| multiome-match-atac-rna-q1Epigenomics | You are given two gzipped TSVs. Rows are features and columns are 8 pseudo-bulk cell populations (same 8 in both files). multiome.match.atac.rna.q1.rna.tsv.gz: RNA TPM (genes × populations). multiome.match.atac.rna.q1.a... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| spatial-sim-q2Spatial | You are given a set of single cell transcriptomic data and Visium spatial transcriptomic data (spatial.sim.tar.gz). The single cell counts matrix is found at spatial_q_sc_counts.csv, and accompanying cell type metadata... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| reverse-encode-q1Epigenomics | For an ENCODE DNase-seq experiment, I started from the filtered BAM produced by the ENCODE4 v3.0.0-alpha.2 (GRCh38/hg38) pipeline. If the experiment had multiple replicates, I pooled all replicate BAMs by concatenating... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| compute-hvg-jaccard-q1Single-cell | Using scanpy and the two AnnData H5AD files below, compute the Jaccard index (similarity) between their HVG. First subset them to common genes using the intersection of all gene names. Use exact string values from adata... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| deleterious-mutation-q1Genomics | In the paired FASTQs deleterious.mutation.q1.R1.fq.gz and deleterious.mutation.q1.R2.fq.gz (exome 2×150 bp, reads from human chr9 only), there is one gene that harbors a high-confidence homozygous nonsense SNV for a gen... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| genome-assembly-contiguity-q1Genomics | In the genome reference file GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna provided, report the N50 (integer, no commas). | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| 1000G-retrieve-genotype-q1Population Genetics | At hg38 chr10:110918899 (1-indexed), find the genotypes of the following individuals from the latest 1000G project data: 'HG01248', 'NA19204', 'NA18614', 'NA21123', 'NA19171', 'HG02303', 'HG01274', 'HG03134', 'NA18639',... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| annotate-variant-regulatory-overlap-q1Epigenomics | Determine the regulatory element that overlap the given variant’s reference span for this specific variant and regulatory resource, without liftover and reporting 1-based inclusive coordinates. Variant: GRCh38, contig c... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| extract-rna-secondary-structure-q1Transcriptomics | Using the ViennaRNA package, determine the minimum free energy secondary structure for the human 5S ribosomal RNA (RNAcentral accession URS0000668495). Output must use dot-bracket notation. After the structure also outp... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| protein-shape-q1Structure | Consider the PDB protein in the file protein.shape.q1.pdb. Which of the following uppercase letters does it resemble most closely: B, D, F, H, J, L, N, P, R, T, V, X, Z? Consider all possible projections and pick the be... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| deg-simple-q2Transcriptomics | I have bulk RNA-seq fastq files from 2 human samples (deg.simple.q2.sampleA.fq.gz, deg.simple.q2.sampleB.fq.gz). There is exactly one gene that has differentially expressed isoforms in the 2 samples. Report the HGNC gen... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| match-genotypes-q1Population Genetics | match.genotypes.q1.tar.gz contains plink genotype files in hg38 for 4 individuals of European ancestry (match.genotypes.1.1.*) and a shuffled metadata table (match.genotypes.1.2.csv) for the same 4 individuals. Please p... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| spatial-sim-q1Spatial | You are given a set of single cell transcriptomic data and Visium spatial transcriptomic data (spatial.sim.tar.gz). The single cell counts matrix is found at spatial_q_sc_counts.csv, and accompanying cell type metadata... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| compute-nonoverlapping-exonic-length-q1Transcriptomics | Compute the total non-overlapping exonic length in base pairs for the mouse gene Lepr using the GENCODE mouse release M31 GTF located at https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| atac-doublet-q1Single-cell | atac.doublet.q1.bed.gz contains a fragment file from a scATAC-seq sample (hg38). Barcodes with low read counts have been filtered out. Look for doublets. Return the coordinates of any one doublet, if any. Respond only w... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| enriched-motif-identification-q1Epigenomics | Consider the DNA sequence provided as dna_with_secret_motif.fasta. Of these motifs, which is the most prevalent? FOXA1, GATA3, MAX, STAT1, OCT4, P53, NANOG, HNF4A, TBP, FOS, MYC, JUN, FOXO1, CTCF, TCF7, SOX2, E2F1, CREB... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| find-deletion-q1Genomics | You are given shallow paired-end whole genome sequencing FASTQ files (find.deletion.r1.fq.gz, find.deletion.r2.fq.gz) simulated from a chromosome of the human genome hg38 which contains a large deletion. Your task is to... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| three-way-barnyard-q1Single-cell | Given paired-end 10x scRNA-seq FASTQs (three.way.barnyard.q1.R1.fq.gz, three.way.barnyard.q1.R2.fq.gz) from a 3-species barnyard (human, mouse, pig)—R1 = 28-bp cell barcode+UMI, R2 = 91-bp cDNA—assume all barcodes are v... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| subtype-inflammation-q1Single-cell | subtype.inflammation.q1.1.mtx.gz and subtype.inflammation.q1.2.mtx.gz contain raw scRNA counts matrices from retinal samples from two eyes of an individual (one per file, each column is a unique barcode that passes QC).... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| read-proportions-q1Genomics | read.proportions.q1.fa contains a synthetic genome with four chromosomes. read.proportions.q1.fq.gz contains 40,000 single-end 36 bp reads drawn from this genome. A read is generated by first picking a chromosome with p... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| sample-swap-atac-q2Single-cell | I have a single-cell ATAC-seq cluster counts pseudobulks lying around from human retinal-associated tissue (sample.swap.atac.q2.tsv.gz). I'm not sure, but I suspect there is a sample swap. Can you check if that is the c... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| exogenous-mix-reads-q1Transcriptomics | I have FASTQ data from a perturbation experiment involving KLF4 exogenous overexpression using a Sendai virus. I want to estimate the fraction of exogenous-origin reads in exogenous.mix.reads.q1.mix.fq, given exogenous.... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| perturb-seq-align-q1Single-cell | perturb.seq.align.q1.ref.h5ad contains a scRNA-seq matrix from a small scale Perturb-seq experiment in a cell type. perturb.seq.align.q1.query.h5ad contains a scRNA-seq matrix from a Perturb-seq experiment using the sam... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gwas-ancestry-q1Population Genetics | Identify the ancestry group which was used to compute these summary statistics in the file gwas.ancestry.q1.tsv.gz. Your answer should be one of the following population codes: AFR (African), ASJ (Ashkenazi Jew), EAS (E... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gene-info-grab-q1Genomics | Consider the gene Hand1. Answer each question with the exact format specified. 1. What is its Ensembl gene ID? (format: ENSMUSGXXXXXXXXXXX, no version suffix) 2. How many amino acids does the canonical protein isoform e... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| genome-coords-q1Epigenomics | You are given a dataset (single_cell_dynamics_question.csv) of time-resolved single-cell measurements from 600 cells, each tracked over 250 consecutive time points. Each row corresponds to one cell at one time point and... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| mystery-peak-set-q1Epigenomics | The file mystery.peak.set.q1.bed.gz contains genomic intervals for six distinct peak sets (S1–S6), all mapped to the hg38 reference genome. Each peak set represents accessible chromatin regions identified under differen... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| phase-chain-q1Population Genetics | Files phase.chain.q1.R1.fq.gz and phase.chain.q1.R2.fq.gz contain exactly 1000 read pairs (2x150) sampled 50:50 from 2 synthetic haplotypes covering a 1.5kb region of hg38. Discover all biallelic SNPs and 1-bp indels in... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| enformer-basic-q1Machine Learning | What is the exact count of the number of parameters in the Enformer model (https://doi.org/10.1038/s41592-021-01252-x). Specifically, report the number of trainable parameters including both the human and mouse heads. F... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| bedtools-ops-q1Epigenomics | In the given ENCODE narrowpeak bed file ENCFF333TAT.bed.gz, convert each interval into a 500bp interval centered at the peak summit. Merge all intervals, and then exclude any that overlaps with the provided blacklist fi... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| orf-annot-q1Genomics | You are given a fasta file containing a human mRNA sequence. Find the main CDS of the sequence, return the start position of the CDS (in a 0-based coordinate system, starting from the first base of the given sequence) a... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| reverse-search-gwas-q2Population Genetics | Identify the PubMed ID of the study from which the summary stats in reverse.search.gwas.q2.gz are derived. Print only the PMID, e.g. 31510655. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| disease-samples-q1Transcriptomics | The file disease.samples.q1.tsv contains bulk RNA-seq TPM data for 9 individuals. Metadata is missing, but the samples are known to be a mix of healthy and diseased subjects. Identify the diseased samples and return the... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| contaminated-rna-q1Transcriptomics | You are given a single end RNA-seq fastq file (contaminated.rna.q1.fq.gz). This file contains mostly human reads and a small fraction of contaminant reads. Identify the contaminant species present. Report the answer as... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| variant-coordinate-lookup-q1Genomics | Retrieve the single base genomic position for the following variant identifiers: rs200533370, rs241311, NM_006492.3:c.595-2A>T, CA548798891, VCV000587372.6, OMIM 616787.0001 on the GRCh38 reference assembly. Report in s... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| histone-chip-q1Epigenomics | I have a histone ChIP-seq ENCODE-style filtered tagAlign file (histone.chip.q1.signal.tagalign.gz) along with its control (histone.chip.q1.control.tagalign.gz), both hg38. I lost the metadata. Can you figure out the his... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| cell-proportions-q1Single-cell | I have a counts matrix of single cell transcriptomic data, cell.proportions.q1.mtx.gz. The data contains measurements from 5350 cells, each with 1000 measured genes. That data was generated by measuring data from a co-c... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| three-way-barnyard-q2Single-cell | Given paired-end 10x scRNA-seq FASTQs (three.way.barnyard.q2.R1.fq.gz, three.way.barnyard.q2.R2.fq.gz) from a 3-species barnyard (human, mouse, pig)—R1=28-bp cell barcode+UMI, R2≈91-bp cDNA. The barcodes are pre-thresho... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| chip-pioneer-q1Epigenomics | chip.pioneer.q1.tar contains fragment bed files obtained by aligning paired-end reads from multiple ChIP-seq experiments and their input controls using the Chromap aligner (v0.2.6, --preset chip, hg38). 6 TFs (TF1-TF6)... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| deleterious-mutation-q2Genomics | In deleterious.mutation.q2.R1.fq.gz (exome 1×150 bp, reads from human 50Mb chunk of chr9 only), there is one gene that harbors a high-confidence nonsense SNV consistent with somatic mosaicism. The gene is highly LoF-int... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| bam-ops-q1Genomics | For the given BAM file mt.sorted.bam, how many reads pass quality threshold of 30 and are properly paired? | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| perturb-seq-effect-q1Single-cell | You are given the cellranger output of a CRISPR perturb-seq experiment in perturb.seq.effect.q1.tar.gz where cell features are at filtered_feature_bc_matrix/features.tsv.gz, counts are at filtered_feature_bc_matrix/matr... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| exogenous-mix-reads-q2Transcriptomics | I have FASTQ data from a perturbation experiment involving KLF4 exogenous overexpression using a Sendai virus. I want to estimate the fraction of exogenous-origin reads in exogenous.mix.reads.q2.mix.fq, given exogenous.... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| align-one-sequence-to-reference-q1Genomics | Where does CACACACAGGAGAT align to in the given GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna? Report as 0-based coordinates in contig:start-end format (no commas). | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| promoter-sequence-retrieval-q1Genomics | Using the Ensembl GRCz11 genome assembly and Ensembl gene annotation, what is the DNA sequence of the promoter region of the zebrafish gene shha? Define the promoter as the region spanning positions −500 to +100 relativ... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| bedtools-chromhmm-q1Epigenomics | We wish to find the chromatin states overlapping the peaks in the given ENCODE narrowpeak bed file ENCFF333TAT.bed.gz. We have a ChromHMM annotation bed file E055_15_coreMarks_dense.bed.gz. What percentage of all bases... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| lung-cancer-sc-q1Single-cell | You are given a single cell transcriptomic counts data generated from primary human tumor samples from patients with lung cancer (lung.cancer.sc.h5ad). This file has been cleaned for doublets and low quality cells alrea... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| tissue-fibroblast-q1Single-cell | I have a counts matrix of transcriptomic reads from a murine multi-tissue fibroblast atlas, tissue.fibroblast.q1.rds. I want to know what tissue the fibroblast corresponding to barcode Cell_11249_MCI is from, and what t... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| characterize-response-q1Transcriptomics | characterize.response.q1.txt contains an ordered list of differentially regulated genes in one direction (decreasing abs log-fold change, all sharing the same sign) in a specific immune cell type in response to a specif... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| geo-lookup-read-matrix-market-q1Single-cell | From the supplementary data of the GEO accession GSE242423, for the D2 scRNA-seq matrix, retrieve the counts for SOX2 for barcode AAACCCAAGTCTTCGA-1. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| annotate-variant-gene-impact-q1Genomics | What is the clinical significance reported in the ClinVar database for the SPI1 variant represented by the HGVS notation NM_003120.3(SPI1):c.143-2A>C? Respond with only the correct cateogry. Answer in all lowercase. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| vcf-infer-build-q1Population Genetics | You are given vcf.infer.build.q1.vcf.gz, a bgzipped VCF containing biallelic SNPs on chromosome 20 for one sample. The VCF has no rsIDs and does not specify a reference build in the header. Determine which reference gen... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gene-pair-ordering-fraction-q1Single-cell | From the dataset at 10x_pbmc68k_reduced.h5ad, consider only CD19+ B cells with percent_mito less than 0.04. Among these, compute the number of cells where expression of gene SRM exceeds that of gene MRPS21 by more than... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| 1000G-retrieve-genotype-q2Population Genetics | I would like to make a file with genotypes at specific loci for all individuals from the 1000G data with 3202 individuals (20201028_3202_raw_GT_with_annot). The positions should be common SNPs- snp151Common from UCSC, h... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| odd-one-out-q1Epigenomics | odd.one.out.q1.tar.gz contains 10 ENCODE-style tagAlign files (hg38). Each file is a different experiment performed in a unique human cell line. 9 experiments were generated using the same assay, however 1 was generated... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gene-expression-query-q1Transcriptomics | Retrieve the median expression level for APOE from the 'Brain_Cortex' samples in the GTEx v8 reference dataset. The value should be in Transcripts Per Million as an integer. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| afgr-1000g-intersect-atac-q1Population Genetics | From the 1000G Phase 3 (3202 individuals), find all individuals that also have ATAC-seq filtered BAMs in the African Functional Genomics Resource (AFGR). Using only publicly available data, collect the md5sums of the fi... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| borzoi-basic-q1Machine Learning | What is the exact count of the number of parameters in any one of the replicates of the Borzoi model (https://doi.org/10.1038/s41588-024-02053-6). Specifically, report the number of trainable parameters including both t... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| annotate-variant-gene-impact-q2Genomics | Using the Ensembl VEP API, determine the consequence for the following variant rs2136714166. Respond with a single word. | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| gene-fusion-q1Transcriptomics | You are given paired-end RNA sequencing FASTQ files (gene.fusion.q1.R1.fq.gz, gene.fusion.q1.R2.fq.gz) from human. The data contains a synthetic gene fusion event. Your task is to identify the fusion genes. Report the a... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| compute-gccontent-promoter-q1Genomics | Compute the GC content of the promoter window for the human transcript ENST00000269305 on assembly GRCh38. Use Ensembl release 115. Define the promoter interval as [TSS - upstream_bp, TSS + downstream_bp - 1] on the tra... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| vcf-infer-ancestry-q1Population Genetics | You are given vcf.infer.ancestry.q1.vcf.gz, a bgzipped VCF containing variants on chromosome 1 for four unrelated individuals: Sample1, Sample2, Sample3, Sample4. Infer each individual’s ancestry as one of: AFR (African... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| find-amplification-q1Genomics | You are given shallow paired-end whole-genome sequencing FASTQ files (find.amplification.R1.fq.gz, find.amplification.R2.fq.gz) simulated from a chromosome of the human genome (hg38) that contains a regional copy-number... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| sample-swap-atac-q1Single-cell | I have bulk ATAC-seq counts lying around from axolotl organs (sample.swap.atac.q1.tsv.gz). Since the genome is large, I broke down standard AmexG_v6.0-DD chromosomes into smaller chunks (sample.swap.atac.q1.chrom.sizes)... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |
| variant-status-q1Transcriptomics | A collaborator sent me variant.status.q1.bam corresponding to a single-end RNA-seq experiment from an individual mapped to hg38. What is the likely variant status at position chrX:154,398,500 (1-based) for this individu... | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 Replicate 2 Replicate 3 3/3 answered | Replicate 1 1/1 answered |