| | --- |
| | configs: |
| | - config_name: default |
| | data_files: |
| | - split: train |
| | path: |
| | - data/files/*/*screenshot*.jpg |
| | - data/files/*/screenshot.jpg |
| | - data/files/*/clusters_*_screenshot_*.jpg |
| | - data/files/*/*.jpg |
| | - data/files/*/*.jpeg |
| | - data/files/*/*.png |
| | - config_name: manifests |
| | data_files: |
| | - split: train |
| | path: |
| | - data/files/*/records.jsonl |
| | - data/files/*/project.json |
| | - data/files/all_records.jsonl |
| | - config_name: structures |
| | data_files: |
| | - split: train |
| | path: |
| | - data/files/*/*.pdb |
| | - data/files/*/*.tpr |
| | - config_name: trajectories |
| | data_files: |
| | - split: train |
| | path: |
| | - data/files/*/*.xtc |
| | - data/files/*/*.trr |
| | - data/files/*/*.dcd |
| | - data/files/*/*.bin |
| | - data/files/*/pca_trajectory_*.bin |
| | license: gpl |
| | task_categories: |
| | - token-classification |
| | tags: |
| | - chemistry |
| | - biology |
| | - medical |
| | - synthetic |
| | size_categories: |
| | - 10K<n<100K |
| | --- |
| | |
| | # DynaRepo MDPosit |
| |
|
| | This repository mirrors Molecular Dynamics (MD) project metadata and files laid out per accession as exposed by Dynarepo. It includes global and per-accession manifests, project-level JSON, and the actual files (structures, trajectories, derived PCA binaries, and analysis screenshots). Field names and shapes follow Dynarepo’s documented model. |
| |
|
| |
|
| | ## Overview |
| |
|
| | ### How to consume |
| |
|
| | - **Stream-parse**: Read the file line-by-line and `json.loads` each object to enumerate replicas and their artifacts. |
| | - **Relate to `project_example.json`**: Each line mirrors an item in `flattened_md_records` and can be joined back to project-level fields if needed. |
| | - **Concatenate across accessions**: You can build a global manifest by concatenating multiple `data\files\<ACCESSION>\records.jsonl` files. |
| | - **Field semantics**: Follow the Dynarepo docs: [Meta](https://dynarepo.inria.fr/#/meta), [Statistics](https://dynarepo.inria.fr/#/statistics), [Help](https://dynarepo.inria.fr/#/help). |
| | |
| | |
| | ## Understanding `all_records.jsonl` (global flattened per-accession manifest) |
| | |
| | - **Source**: Global, line-delimited aggregation of per-replica records across all accessions. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help). |
| | - **Where it lives**: `data\files\all_records.jsonl`. |
| | - **What it is**: A JSON Lines file where each line mirrors a single replica entry from per-accession `records.jsonl` (fields include `project_identifier`, `accession`, `md_index`, `md_name`, `analyses`, `metadata`, and `files`). |
| | - **How to use**: Stream-parse line by line, filter by `accession` or `analyses`, and group by `accession`/`md_index` to enumerate all replicas and their artifacts across the dataset. Field semantics are identical to per-accession records and follow Dynarepo docs. |
| | |
| | ## Remote folder contents in `data\files\<ACCESSION>` (A0098 example) |
| | |
| | - **Source**: Mirrors the per-accession file repository exposed by Dynarepo. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help). |
| | - **Where it appears**: Under `data\files\<ACCESSION>\` in this repository; corresponds to Dynarepo’s remote path `/projects/<ACCESSION>/files`. |
| | - **What you will typically find** (A0098 shown): |
| | - Core descriptors: `project.json` (~5.18 kB), `records.jsonl` (~43.3 kB) |
| | - Core MD simulation assets: `topology.tpr` (~1.71 MB), `structure.pdb` (~397 kB), `trajectory.xtc` (~93.5 MB), `trajectory.bin` (~294 MB) |
| | - PCA-derived binaries: `pca_trajectory_01.bin` … `pca_trajectory_05.bin` (5 files, ~237 kB each) |
| | - Cluster analysis screenshots: |
| | - `clusters_00_screenshot_00.jpg` … `clusters_00_screenshot_20.jpg` (21 images, ~16–21 kB each) |
| | - `clusters_01_screenshot_00.jpg` … `clusters_01_screenshot_19.jpg` (20 images, ~16–21 kB each) |
| | - Cover/preview: `screenshot.jpg` (~20.7 kB) |
| | - **Relationship to manifests**: |
| | - Every file present under `data\files\<ACCESSION>\` is enumerated in that accession’s `records.jsonl` `files[]` entries with `name`, `downloadUrl` (relative to `/projects/<ACCESSION>/files/<name>`), `length` (bytes), and `contentType`. |
| | - The same inventory is summarized in `project.json` under its `files` section (e.g., `list`, `filenotes`, `merged`) and joined into `flattened_md_records` for per-replica views. |
| | - **Notes**: Exact counts and sizes vary by accession and by which analyses were run; additional analysis types will add further artifacts alongside those listed above. |
| | |
| | ## Understanding `project.json` (Dynarepo dataset A0098) |
| | |
| | - **Source**: Dataset metadata follows the Dynarepo model. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help). |
| | - **Where it appears**: Each dataset under `data\files\<ACCESSION>` includes a project-level JSON with this schema. This repository provides a canonical example in `project_example.json`. |
| | - **What it is**: A single, self-contained description of an MD project combining high-level project metadata, per-replica MD records, file inventory, topology, references, analysis results, and summaries. It is designed to be directly consumable by Dynarepo services and UIs. |
| | |
| | ### High-level structure |
| | |
| | - **`project`**: Core project info and global metadata |
| | - Keys: `accession`, `published`, `metadata` (e.g., `NAME`, `DESCRIPTION`, `AUTHORS`, `PROGRAM`, `VERSION`, `TYPE`, `METHOD`, `LICENSE`, `PDBIDS`, `REFERENCES`, simulation params like `FRAMESTEP`, `TIMESTEP`, `TEMP`, `ENSEMBLE`, `FF`, `WAT`, box sizes, system counts), `mds` (replica names), `analyses` (available analysis types), `files` (canonical file names), `mdIndex`/`mdNumber`/`refframe`. |
| | - **`flattened_md_records`**: One entry per MD replica with the replica’s `metadata` and a resolved `files` list including `downloadUrl`, `length`, and `contentType`. |
| | - **`files`**: |
| | - `list`: canonical file names present in the project |
| | - `filenotes`: storage-level details (size, content type, upload date) |
| | - `merged`: convenient join of name, URL, size, and metadata |
| | - **`topology`**: Atoms, residues, chains, bonding, and external references used to build the system. |
| | - **`references`**: Protein and PDB references (e.g., UniProt IDs, sequences, domains) and cross-links to PDB entries. |
| | - **`analyses`**: Machine-readable outputs per analysis (e.g., `clusters`, `dist-perres`, `energies`, `fluctuation`, `hbonds`, `interactions`, `pca`, `pockets`, `rgyr`, `rmsd*`, `sasa`, `tmscores`). |
| | - **`summaries`**: Compact keys/metrics for quick inspection and validation. |
| | |
| | ### How this maps to datapoint A0098 |
| | |
| | - **Accession**: `A0098` (see `data\files\A0098\records.jsonl` for the per-replica lines used to populate `flattened_md_records`). |
| | - **Project metadata examples** (from A0098): |
| | - `metadata.NAME`: "Dynarepo 5FZT" |
| | - `metadata.PDBIDS`: `["5FZT"]` |
| | - `metadata.REFERENCES`: `["P26039", "Q96QB1"]` |
| | - Simulation constants: `FRAMESTEP: 0.1`, `TIMESTEP: 2`, `TEMP: 310`, `ENSEMBLE: "NPT"`, `FF: ["CHARMM36m"]`, `WAT: "TIP3P"`, `BOXTYPE: "Dodecahedron"` |
| | - System scale: `mdFrames: 5001`, `mdAtoms: 4900`, `PROTRES: 329`, `SYSTATS: 4900` |
| | - **Files commonly present**: `topology.tpr`, `structure.pdb`, `trajectory.xtc`, `trajectory.bin`, `pca_trajectory_*.bin`, and analysis screenshots (e.g., `clusters_*_screenshot_*.jpg`). |
| | - **Analyses present**: `clusters`, `clusters-00`, `clusters-01`, `dist-perres`, `energies`, `fluctuation`, `hbonds`, `interactions`, `pca`, `rgyr`, `rmsd-pairwise`, `rmsd-perres`, `rmsds`, `sasa`, `tmscores`. |
| | |
| | ## Understanding `records.jsonl` (per-replica manifest in `data\files\<ACCESSION>`) |
| | |
| | - **Source**: Per-MD replica records consistent with Dynarepo’s flattened MD model. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help). |
| | - **Where it appears**: For each accession, a `records.jsonl` lives under `data\files\<ACCESSION>\`. This repository includes `data\files\A0098\records.jsonl`. A compact illustration is also provided at the repository root as `records._examplejsonl`. |
| | - **What it is**: A JSON Lines file; each line describes one MD replica and its files. |
| | |
| | ### Record shape (keys you will see per line) |
| | |
| | - **Top-level identifiers**: `project_identifier`, `accession`, `published` |
| | - **Replica info**: `md_index` (0-based), `md_name` (e.g., "replica 1"), `chains` (if applicable) |
| | - **Analyses available**: `analyses` (e.g., `clusters`, `rmsds`, `pca`, `sasa`, ...) |
| | - **`metadata` object**: Biology and simulation parameters used by Dynarepo UIs and services. Common fields include `NAME`, `DESCRIPTION`, `AUTHORS`, `GROUPS`, `CONTACT`, `PROGRAM`, `VERSION`, `TYPE`, `METHOD`, `LICENSE` (and `LINKCENSE`), `PDBIDS`, `REFERENCES`, sequences/domains (`PROTSEQ`, `NUCLSEQ`, `DOMAINS`), simulation setup (`FRAMESTEP`, `TIMESTEP`, `TEMP`, `ENSEMBLE`, `FF`, `WAT`, `BOXTYPE`), system sizes (`SYSTATS`, `SYSTRES`, `PROTATS`, `PROTRES`, ...), optional `INTERACTIONS`, box sizes (`BOXSIZEX/Y/Z`), and per-replica summaries like `mdAtoms` and `mdFrames`. |
| | - **`files` array**: One entry per stored artifact with `name`, `downloadUrl` (relative to `/projects/<ACCESSION>/files/<name>`), `length` (bytes), `contentType`, and a small `metadata` dict (e.g., `{project: <id>, md: <index>}` or per-file stats for derived binaries). |
| | |
| | Typical files for A0098 include `topology.tpr`, `structure.pdb`, `trajectory.xtc`, `trajectory.bin`, `pca_trajectory_*.bin`, and analysis screenshots like `clusters_*_screenshot_*.jpg`. |
| | |
| | ### Example (A0098, truncated line 1) |
| | |
| | ```json |
| | { |
| | "project_identifier": "A0098", |
| | "accession": "A0098", |
| | "published": true, |
| | "md_index": 0, |
| | "md_name": "replica 1", |
| | "analyses": ["clusters", "pca", "rmsds", "sasa", "..."], |
| | "metadata": { |
| | "NAME": "Dynarepo 5FZT", |
| | "PDBIDS": ["5FZT"], |
| | "FRAMESTEP": 0.1, |
| | "TIMESTEP": 2, |
| | "TEMP": 310, |
| | "ENSEMBLE": "NPT", |
| | "FF": ["CHARMM36m"], |
| | "WAT": "TIP3P", |
| | "mdAtoms": 4900, |
| | "mdFrames": 5001 |
| | }, |
| | "files": [ |
| | {"name": "topology.tpr", "downloadUrl": "/projects/A0098/files/topology.tpr", "length": 1712912, "contentType": "application/octet-stream"}, |
| | {"name": "structure.pdb", "downloadUrl": "/projects/A0098/files/structure.pdb", "length": 396935, "contentType": "chemical/x-pdb"}, |
| | {"name": "trajectory.xtc", "downloadUrl": "/projects/A0098/files/trajectory.xtc", "length": 93513296, "contentType": "application/octet-stream"} |
| | // ... more files omitted ... |
| | ] |
| | } |
| | ``` |
| | |
| | |
| | ### Contributing |
| | |
| | When creating a new project JSON for another accession, minimally review/update: |
| | |
| | - **Identifiers**: `project.accession`, `project.identifier`, and `metadata.NAME` |
| | - **Biology**: `metadata.PDBIDS`, `metadata.REFERENCES` (UniProt), sequences/domains in `references` |
| | - **Simulation**: `FRAMESTEP`, `TIMESTEP`, `TEMP`, `ENSEMBLE`, `FF`, `WAT`, box sizes, atom/residue counts |
| | - **Replicas**: `mds` list and `flattened_md_records[*].md_index/md_name` |
| | - **Files**: Ensure `files.list`, `files.merged`, and each replica’s `files[]` match your storage paths and sizes |
| | - **Analyses**: Keep only the analyses you actually produced and include their data payloads |
| | |
| | For reference on field meanings and expected shapes, consult the Dynarepo documentation: [Meta](https://dynarepo.inria.fr/#/meta), [Statistics](https://dynarepo.inria.fr/#/statistics), [Help](https://dynarepo.inria.fr/#/help). |
| | |
| | |
| | **References**: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), [Dynarepo Help](https://dynarepo.inria.fr/#/help) |
