You can work from a project folder, connect source folders, attach supported files to a conversation, or give OpenScience a URL or database identifier. Choose the path that preserves the original material and gives the task enough context.
Ways to provide material
| Method | Best for | Start here |
|---|---|---|
| Connect a source folder | Existing research collections and code | Projects. |
| Attach a file | A small input for the current conversation | Use the composer's attachment picker. |
| Mention a project path | Material already available to the project | Select a file through @ or state its exact path. |
| Give a URL | A known paper, page, or documentation reference | Documents and Research search. |
| Give a database and accession | Scientific records and downloadable formats | Database workflows. |
| Connect an external service | Tools or records supplied through that integration | MCP connectors. |
The attachment picker accepts supported files up to 20 MiB per file. For larger datasets or collections, use project/source folders and ask for a bounded inspection first. If browser storage cannot hold a large attachment, the app keeps it only in the current tab and warns that the draft is not saved in this browser; send it before you reload rather than relying on the draft. An accepted file type is not a guarantee that the selected model directly understands every part of its contents.
Documents and images
| Type | Working with it |
|---|---|
| Read and compare papers; open the page preview to verify source material. Scanned pages may need text extraction. | |
| Markdown and plain text | Protocols, notes, handoffs, reports, and instructions; inspect source or rendered Markdown. |
| HTML | Preview an available local document and inspect its source. |
| LaTeX | Edit source and inspect mathematical expressions; producing a complete PDF requires a suitable compiler. |
| PNG, JPEG, GIF, WebP | Attach supported images; interpretation depends on the selected model and available tools. |
| Other supported image previews | Files can also preview formats such as SVG, BMP, and AVIF. Preview support and attachment support are different. |
Use Reading and extracting documents for extraction, and Figures for data-driven visuals.
Tables, notebooks, and code
| Type | Working with it |
|---|---|
| CSV, TSV | Explore rows, columns, missing values, and numeric distributions. |
| JSON arrays, JSONL, NDJSON | Inspect record-oriented data in the table explorer. Other JSON opens as source. |
| Python, R, Julia, and other source files | Read, edit, and run with the relevant available language tools. |
Jupyter notebooks (.ipynb) | Preview Markdown and code cells with saved text, images, tables, and errors; use Edit for JSON source. |
R Markdown and Quarto (.Rmd, .qmd) | Preview prose and fenced code chunks, including referenced figures; use Edit for source. |
| YAML, TOML, XML, and text configuration | Inspect and edit source with the schema or application requirements in mind. |
| Excel or another application-specific format | Keep the original and use available analysis software to read or convert it. Native spreadsheet editing is not the table preview's role. |
Specify delimiters, encoding, sheet names, dates, and missing-value markers when known. See Tables and datasets.
In a research session, use Run on a Python or R cell to execute it in that session's local kernel. Cells share the corresponding runtime's variables; install the required interpreter and dependencies first. Project execution permissions still apply. Opening a document never executes code. New outputs are labelled Run output · not saved and remain in that preview; editing and saving the source is separate. Use Compute to inspect or interrupt the runtime.
The document preview shows Jupyter v4 saved outputs and renders Markdown with code chunks. It does not run a full Quarto/knitr build, evaluate inline expressions, or invent outputs that are absent from an R Markdown or Quarto source file. For those formats, existing figures referenced in Markdown render in place. Other chunk languages remain visible with execution marked unavailable.
Scientific formats
| Material | Recognized formats or views |
|---|---|
| Protein structures | PDB, ENT, CIF/mmCIF, PDBQT, GRO. |
| Small molecules | SDF, MOL, MOL2, XYZ; SMILES for 2D depictions. |
| Sequences and alignments | FASTA-family sequence files; equal-length multiple records can open as an alignment. |
| Sequencing reads | FASTQ/FQ summary and quality inspection. |
| Variants and annotations | VCF, BED, GFF/GFF3, GTF. |
| Alignments | SAM summaries; BAM and CRAM inspection with required local tools. |
| Single-cell data | H5AD and Loom inspection; available stored embeddings can be visualized. |
| Mass spectrometry | mzML summary inspection. |
Scientific viewers explains what each view actually shows, prerequisites, and when a preview represents only a sample.
Make an input usable
Include its meaning, not just its filename:
Read data/assay.tsv. Each row is one biological sample; concentration is
in micromolar and response is background-corrected fluorescence. The
column batch identifies the experiment day. Preserve the source file and
report missing values before fitting anything.
For a collection of papers, include the question and inclusion criteria. For code, include the command that failed and expected behavior. For a structure, include the organism, chain or ligand of interest, and the scientific question.
Keep source and derived files separate
Save transformations as new files with the script that produced them. Keep original accession identifiers, download dates, units, and reference versions in a methods note. Use Saved Results for outputs you want to retain and Files and storage for backup and export.