Add the summary config (one row per trajectory) and the Cellarium QC crosswalk

data/summary/<family>/part-00000.parquet: n_steps and mean/min/max/first/last of the 18 scalars per trajectory, computed from core at 1 s (ADR 0010); 117,174 rows, verified against index.parquet (one row per located core trajectory, n_steps == core_n_rows). README.md re-rendered with card.render: summary config in front matter and tables, termination_class to Cellarium qc crosswalk under Outcomes. manifest.json gains configs.summary.

README.md

@@ -12,6 +12,18 @@ size_categories:
 configs:
 - config_name: index
   data_files: index.parquet
+- config_name: summary
+  data_files:
+  - split: wildtype_media
+    path: data/summary/wildtype_media/*.parquet
+  - split: single_knockout
+    path: data/summary/single_knockout/*.parquet
+  - split: dynamic_media
+    path: data/summary/dynamic_media/*.parquet
+  - split: regulation
+    path: data/summary/regulation/*.parquet
+  - split: double_knockout
+    path: data/summary/double_knockout/*.parquet
 - config_name: core
   data_files:
   - split: wildtype_media
@@ -53,13 +65,13 @@ Time series from the [wcEcoli](https://github.com/CovertLab/wcEcoli) whole-cell
 
 Which families of each config are uploaded here (size on the Hub):
 
-| family | trajectories | `core` | `expression` | `metabolism` | `expression_1s` | `metabolism_1s` |
-|---|---:|---|---|---|---|---|
-| `wildtype_media` | 641 | yes (103.0 MB) | yes (512.4 MB) | yes (502.3 MB) | not in this release | not in this release |
-| `single_knockout` | 83,937 | yes (13.5 GB) | not yet | not yet | not in this release | not in this release |
-| `dynamic_media` | 18,599 | yes (2.8 GB) | not yet | not yet | not in this release | not in this release |
-| `regulation` | 2,046 | yes (323.9 MB) | not yet | not yet | not in this release | not in this release |
-| `double_knockout` | 11,951 | yes (1.9 GB) | not yet | not yet | not in this release | not in this release |
+| family | trajectories | `summary` | `core` | `expression` | `metabolism` | `expression_1s` | `metabolism_1s` |
+|---|---:|---|---|---|---|---|---|
+| `wildtype_media` | 641 | yes (205.1 KB) | yes (103.0 MB) | yes (512.4 MB) | yes (502.3 MB) | not in this release | not in this release |
+| `single_knockout` | 83,937 | yes (20.2 MB) | yes (13.5 GB) | not yet | not yet | not in this release | not in this release |
+| `dynamic_media` | 18,599 | yes (5.2 MB) | yes (2.8 GB) | not yet | not yet | not in this release | not in this release |
+| `regulation` | 2,046 | yes (623.0 KB) | yes (323.9 MB) | not yet | not yet | not in this release | not in this release |
+| `double_knockout` | 11,951 | yes (3.4 MB) | yes (1.9 GB) | not yet | not yet | not in this release | not in this release |
 
 `expression` and `metabolism` are currently available for `wildtype_media` only; `single_knockout`, `dynamic_media`, `regulation` and `double_knockout` will be added in a later upload. `expression_1s` and `metabolism_1s` (1 s matrices, ~1.3 TB estimated) are not in this release.
 
@@ -67,10 +79,11 @@ Which families of each config are uploaded here (size on the Hub):
 
 ## Configs
 
-Each config is one data product. Every config carries `sample_id`, `t`, `t_abs` and the 18 scalar channels; the matrix configs add per-gene or per-reaction columns. `expression` and `metabolism` keep the rows with `t % 10 == 0` plus each trajectory's last row (point samples, not averages); `expression_1s` and `metabolism_1s` keep every row. The split of every config is the family.
+Each config is one data product. `summary` is one row per trajectory and joins to `index.parquet` on `sample_id`: `n_steps` and, for each of the 18 scalar channels in the order of the product schema, `<channel>_mean`, `_min`, `_max`, `_first` and `_last` over the trajectory's 1 s `core` rows (int32 for `mrna_counts` and `n_oric` except `_mean`, float32 otherwise; the `growth_rate` statistics skip its null row 0, so `growth_rate_first` is the value at t = 1). Every other config carries `sample_id`, `t`, `t_abs` and the 18 scalar channels; the matrix configs add per-gene or per-reaction columns. `expression` and `metabolism` keep the rows with `t % 10 == 0` plus each trajectory's last row (point samples, not averages); `expression_1s` and `metabolism_1s` keep every row. The split of every config is the family.
 
 | config | rows every | matrices (active columns) | trajectories | rows | size |
 |---|---|---|---:|---:|---:|
+| `summary` | trajectory | none: `n_steps` and `_mean`, `_min`, `_max`, `_first`, `_last` of each scalar | 117,174 | 117,174 | 29.6 MB |
 | `core` | 1 s | scalars only | 117,174 | 316,751,845 | 18.6 GB |
 | `expression` | 10 s | `mrna_counts_matrix` (2,773), `protein_counts_matrix` (4,174) | 641 (wildtype_media only) | 173,523 | 512.4 MB |
 | `metabolism` | 10 s | `reaction_flux_matrix` (3,974), `exchange_flux_matrix` (82) | 641 (wildtype_media only) | 173,523 | 502.3 MB |
@@ -231,6 +244,19 @@ assert table.num_rows == row["expression_n_rows"]
 
 `time_limit` is the only clean non-division; the other classes are solver failures, and the rows before the failure are kept as recorded.
 
+The same outcomes in the `qc` vocabulary of the Cellarium corpus:
+
+| well4cell `termination_class` | Cellarium `qc` | meaning |
+|---|---|---|
+| `none` | `ok` | the cell divided |
+| `time_limit` | `no_division` | the generation ran to the time limit without dividing; the model's "did not divide" |
+| `negative_counts` | `crashed` | simulator error (a molecule count went negative) |
+| `fba_infeasible` | `fba_infeasible` | metabolism solver failure |
+| `equilibrium_unstable` | `crashed` | equilibrium solver failure |
+| `other` | `crashed` | any other simulator error |
+
+Only `time_limit` is a prediction of the model about the cell; the other non-`none` classes are numerical failures of the simulation, and a viability task should treat them as such. Cellarium's `implausible_channel`, `over_replicated` and `translation_collapse` have no counterpart here because well4cell does not run those checks; its vocabulary is defined in the Cellarium repository's `docs/QC_STATUSES.md` (https://github.com/evanniko1/cellarium).
+
 ## Suggested tasks
 
 1. **Growth-rate regression from the perturbation**: predict `growth_rate` (index) from the perturbation columns (`knockout_genes`, media, `tf_target`, ...) and optionally the first rows of the trajectory.

data/summary/double_knockout/part-00000.parquet

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+size 3356859

data/summary/dynamic_media/part-00000.parquet

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data/summary/regulation/part-00000.parquet

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data/summary/single_knockout/part-00000.parquet

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+size 20202224

data/summary/wildtype_media/part-00000.parquet

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manifest.json

@@ -1 +1 @@
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