OpenScience can retrieve supported biological records, inspect sequence and genomic formats, and help implement an analysis with available scientific software. Begin with the organism, reference version, input format, and question.
Select the starting point
| Input | First task |
|---|---|
| Gene or protein name | Resolve the intended organism and accession in a scientific database. |
| FASTA sequences | Check identifiers, alphabet, lengths, gaps, and duplicate records. |
| FASTQ reads | Inspect read quality, lengths, invalid records, and whether the preview is sampled. |
| VCF variants | Confirm reference assembly, samples, filtering, and variant representation. |
| BED/GFF/GTF annotations | Verify assembly, coordinate convention, feature type, and chromosome naming. |
| SAM/BAM/CRAM alignments | Check references, alignment status, indexes, and tool availability. |
| H5AD or Loom | Inspect dimensions, annotations, stored layers, and available embeddings. |
Inspect before transforming
Inspect data/reads.fastq and methods/sample-sheet.csv. Check sample names,
read lengths, quality summaries, and whether the inspection covers the
full file. Save a report and propose the next quality-control step before
filtering or discarding reads.
Use the scientific viewers for an initial visual check, then request full-file calculations where appropriate. Preserve failed or excluded records in a separate report.
Keep reference assumptions explicit
Record the reference assembly, annotation release, identifier version, and coordinate convention in the analysis. Do not silently combine a variant file from one assembly with annotations from another.
For sequence comparisons, state whether the input is nucleotide or protein sequence, which records are included, and whether an existing alignment is trusted or must be recomputed.
Work with single-cell data
Inspect data/cells.h5ad without changing it. Summarize cell and feature
counts, available annotations, layers, and stored embeddings. Ask which
layer represents counts and which preprocessing has already been done.
Propose quality-control and analysis steps before applying them.
An existing embedding is an analysis output, not evidence that the preprocessing or cluster interpretation is correct. Keep sample-level structure and experimental design visible when comparing groups.
Choose skills and tools
Search the skill directory for the organism, assay, or method. Check Tools for readiness and prerequisites before asking for a pipeline. Biopython has a supported setup path; other specialized packages may require a separate reviewed environment. With an NVIDIA API key connected, Evo 2 (the BioNeMo genomic foundation model NIM) is available through the scientific-capability tool for sequence generation and scoring.
Larger workloads can use compute jobs. Begin with a pilot, preserve commands and versions, and retrieve the full output set.
Deliver a reusable result
Ask for original source identifiers, input/reference versions, quality-control summaries, transformation code, output paths, and limitations. Keep biological interpretation separate from the software's raw output, and save the reviewed report as a Result.