What RxCubed is
A plain-language overview of the workspace, its navigation, and how evidence is organised.
What RxCubed is
RxCubed is a guided workspace for collecting, understanding, and analysing research evidence. Find papers, collect biological and chemical files, run computational tools, and keep each result connected to its source.
The top navigation
The project navigation follows the workflow, but nothing is locked or required in a particular order:
- Dashboard — the project home and progress overview.
- Find papers — Literature Search (OpenAlex) and paper upload.
- Collect files — connectors such as RCSB PDB, PubChem, UniProt, AlphaFold DB, ChEMBL, and InterPro, plus file upload.
- Model — Tool Selector and the computational tools available to you.
- Create reports — reports and document upload.
- Results Hub — one place to browse everything saved or generated.
The AI Assistant and project Notes are available from the side panels. The assistant explains pages and evidence; it does not click buttons or run work for you.
Three levels of organisation
Results are arranged consistently at three levels:
Category → Tool → Run
- Category is the broad area, such as Literature, File Collection, Model, or Documents.
- Tool is the specific source or operation, such as OpenAlex, RCSB PDB, or Structure Alignment.
- Run is one search or tool execution. Collection runs include the query and timestamp; computational runs have their editable run name and timestamp.
A run can hold several evidence rows — a database record saved as more than one file type, or a tool that writes more than one output. Rows that belong together stay next to each other under their run; each keeps its own file type and provenance.
Evidence and provenance
Evidence includes saved papers, database records, files, computational outputs, and reports. Each row keeps its source, metadata, file (when available), and provenance. Derived results point to their inputs, so you can trace a result backward and see what was built from it.
Results Hub in brief
Four tabs: Browse, Missing Files, Search, and Graph.
Browse presents evidence grouped by Category, Tool, and Run. The right-hand Tools & runs navigator selects the portion shown in the middle.
Missing Files lists evidence whose file could not be downloaded, so you can attach it by hand. Search looks across all the project's evidence by name.
Graph starts empty. Select a run in the right navigator to see that run's direct and indirect upstream inputs and downstream results. Clicking a graph node only updates the detail panel; it does not replace the focused run or remove its graph. The graph and Browse view use the same evidence and provenance data.
Writing levels
Chat is private to you. Notes are shared project-level working documents. Evidence and reports are persistent, checksummed records with provenance.