well4cell 1.0.0-rc1: readme

README.md

@@ -60,11 +60,35 @@ configs:
     path: data/metabolism/regulation/*.parquet
   - split: double_knockout
     path: data/metabolism/double_knockout/*.parquet
+- config_name: expression_1s
+  data_files:
+  - split: wildtype_media
+    path: data/expression_1s/wildtype_media/*.parquet
+  - split: single_knockout
+    path: data/expression_1s/single_knockout/*.parquet
+  - split: dynamic_media
+    path: data/expression_1s/dynamic_media/*.parquet
+  - split: regulation
+    path: data/expression_1s/regulation/*.parquet
+  - split: double_knockout
+    path: data/expression_1s/double_knockout/*.parquet
+- config_name: metabolism_1s
+  data_files:
+  - split: wildtype_media
+    path: data/metabolism_1s/wildtype_media/*.parquet
+  - split: single_knockout
+    path: data/metabolism_1s/single_knockout/*.parquet
+  - split: dynamic_media
+    path: data/metabolism_1s/dynamic_media/*.parquet
+  - split: regulation
+    path: data/metabolism_1s/regulation/*.parquet
+  - split: double_knockout
+    path: data/metabolism_1s/double_knockout/*.parquet
 ---
 
 # The Well for The Cell
 
-Version **1.0.0-rc1**, built 2026-10-21T02:31:02+00:00 from wcEcoli commit `f3bdabc004a473964df62712469213bffde7ab90`.
+Version **1.0.0-rc1**, built 2026-10-21T23:05:48+00:00 from wcEcoli commit `46667c5237081d72ed1195ec9f7332cd21b3be5d`.
 
 Time series from the [wcEcoli](https://github.com/CovertLab/wcEcoli) whole-cell model of *Escherichia coli*. Each sample is **one cell generation**: the cell from birth to division (or to the step at which the simulation stopped), recorded every **1 s** of simulated time. Lineages are simulated for several generations, and the samples of one lineage are linked by `parent_id`. The 117,174 trajectories come from 31,101 lineages of 3,896 distinct cells (design x condition), grouped into five families by campaign tier.
 
@@ -83,13 +107,13 @@ Which families of each config are uploaded here (size on the Hub):
 
 | family | trajectories | `summary` | `core` | `expression` | `metabolism` | `expression_1s` | `metabolism_1s` |
 |---|---:|---|---|---|---|---|---|
-| `wildtype_media` | 641 | yes (242.6 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 (23.9 MB) | yes (13.5 GB) | yes (59.9 GB) | yes (65.6 GB) | not in this release | not in this release |
-| `dynamic_media` | 18,599 | yes (6.2 MB) | yes (2.8 GB) | yes (11.7 GB) | yes (13.5 GB) | not in this release | not in this release |
-| `regulation` | 2,046 | yes (736.0 KB) | yes (323.9 MB) | yes (1.7 GB) | yes (1.6 GB) | not in this release | not in this release |
-| `double_knockout` | 11,951 | yes (4.0 MB) | yes (1.9 GB) | yes (8.8 GB) | yes (9.1 GB) | not in this release | not in this release |
+| `wildtype_media` | 641 | yes (242.6 KB) | yes (103.0 MB) | yes (512.4 MB) | yes (502.3 MB) | yes (2.0 GB) | yes (4.9 GB) |
+| `single_knockout` | 83,937 | yes (23.9 MB) | yes (13.5 GB) | yes (59.9 GB) | yes (65.6 GB) | yes (237.4 GB) | yes (639.3 GB) |
+| `dynamic_media` | 18,599 | yes (6.2 MB) | yes (2.8 GB) | yes (11.7 GB) | yes (13.5 GB) | yes (46.4 GB) | yes (131.6 GB) |
+| `regulation` | 2,046 | yes (736.0 KB) | yes (323.9 MB) | yes (1.7 GB) | yes (1.6 GB) | yes (6.5 GB) | yes (15.6 GB) |
+| `double_knockout` | 11,951 | yes (4.0 MB) | yes (1.9 GB) | yes (8.8 GB) | yes (9.1 GB) | yes (35.0 GB) | yes (88.9 GB) |
 
-`expression_1s` and `metabolism_1s` (1 s matrices, ~1.3 TB estimated) are not in this release.
+Every config is complete: all five families are in this repo.
 
 `index.parquet` lists every trajectory, uploaded or not. Its locator columns (`<config>_file`, `<config>_row_offset`, `<config>_n_rows`) are null for data not in this repo, so `index["<config>_file"].notnull()` (e.g. `index.expression_file.notnull()`) is the authoritative availability check. `load_dataset(..., "<config>", split="<family>")` fails for a family that has not been uploaded (e.g. `load_dataset(..., "expression", split="single_knockout")` until that family is uploaded).
 
@@ -103,8 +127,8 @@ Each config is one data product. `summary` is one row per trajectory and joins t
 | `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) | 117,174 | 31,830,394 | 82.7 GB |
 | `metabolism` | 10 s | `reaction_flux_matrix` (3,974), `exchange_flux_matrix` (82) | 117,174 | 31,830,394 | 90.3 GB |
-| `expression_1s` | 1 s | `mrna_counts_matrix` (2,773), `protein_counts_matrix` (4,174) | not in this release | | |
-| `metabolism_1s` | 1 s | `reaction_flux_matrix` (3,974), `exchange_flux_matrix` (82) | not in this release | | |
+| `expression_1s` | 1 s | `mrna_counts_matrix` (2,773), `protein_counts_matrix` (4,174) | 117,174 | 316,751,845 | 327.4 GB |
+| `metabolism_1s` | 1 s | `reaction_flux_matrix` (3,974), `exchange_flux_matrix` (82) | 117,174 | 316,751,845 | 880.3 GB |
 
 Matrix columns are pruned to the columns that are non-zero at least once anywhere in the campaign (active columns: mrna_counts 2,773 of 3,133, protein_counts 4,174 of 4,310, reaction_flux 3,974 of 9,612, exchange_flux 82 of 87). The full column lists, with an `active` mask and each active column's position in the product (`product_column`), are in `provenance/reference/<matrix>.parquet`.
 
@@ -292,7 +316,7 @@ Use `split_by_lineage` (train 93,698 / val 11,731 / test 11,745) to hold out who
 - Every trajectory ran with operons on and the steady-state tRNA charging model (`trna_charging` true, no kinetic charging), from one of two fitted parameter sets identified by `kb_sha256` and `parca_cache`; do not pool rows across the two parameter sets without checking `kb_sha256`.
 - `provenance/scan_runs.parquet`: every run directory read (32,072 runs), with its generation count and reference-id hash.
 - `provenance/failed_jobs.parquet`: 971 campaign jobs that failed, with the error message and the generations they left behind.
-- `provenance/export_qc.parquet`: the QC verdict of every trajectory in every config (351,522 checks, 0 failed). Trajectories that fail QC are left out of that config.
+- `provenance/export_qc.parquet`: the QC verdict of every trajectory in every config (585,870 checks, 0 failed). Trajectories that fail QC are left out of that config.
 - `stats/<family>.parquet`: per product, channel and matrix column: mean, population std, min, max and row count.
 - `manifest.json`: row and byte totals per config, counts per family.