@rho-workspace/rho 0.5.2 → 0.5.4

package/docs/HEADLESS.md

@@ -37,23 +37,39 @@ it. Missing browser renderers do not disable the headless protocol.
 ## Install and start
 
 The selected baseline is macOS arm64, Node 22.22.3 (engine range
-`>=22.22.0 <23`), npm 10.9.8, Python 3 with `fcntl`, and Rscript 4.5.2. Windows x64
+`>=22.22.0 <27`; the suite and the installed check also passed on Node 24.22.2 and
+26.13.0), npm 10.9.8, Python 3 with `fcntl`, and Rscript 4.5.2. Windows x64
 was checked with Node 22.23.4 and Rscript 4.5.1; its writer lock needs no Python, and
 there `rho.cmd` starts Rho and Ctrl+Break on its console stops it in order.
-The unsigned local tarball contains Plugins and the selected digest-checked Core
-binary. R and any project-selected packages are external prerequisites, and so are
-the Agent clients: conversations drive the person's installed Claude Code or Codex.
+The unsigned npm package `@rho-workspace/rho` contains Plugins and one digest-checked Core
+binary for each of macOS arm64, Linux x64 and arm64 and Windows x64; CI installs it on each.
+R and any project-selected packages are external prerequisites, and so are the Agent
+clients: conversations drive the person's installed Claude Code or Codex.
 The service, documents, declared files and saved resource readers work without R.
 An unavailable Rscript returns an unknown dependency probe and prevents managed R execution.
-Other platforms and npm registry publication are unverified.
+Other platforms are unverified.
 
 ```sh
-npm install --prefix /absolute/install /absolute/rho-workspace-rho-0.5.2.tgz
-/absolute/install/node_modules/.bin/rho \
-  --root /absolute/projects --state-dir /absolute/service-state
+npm install -g @rho-workspace/rho
+rho --root /absolute/projects --state-dir /absolute/service-state
 ```
 
 Create the allowed projects directory first. Keep service state outside projects.
+
+A person who has no folders to name runs the package with no arguments instead (from
+0.5.4; 0.5.3 prints its usage and exits 2):
+
+```sh
+npx @rho-workspace/rho
+```
+
+That start uses `~/Rho/projects` and `~/Rho/state`, creates both, ships the example
+project on a new state, and prints — after the machine line — the address to open,
+the two folders, and whether the Agent client and R were found, so a missing one is
+read at startup rather than discovered later. It opens the address in a browser when
+stdout is an interactive terminal. Every flagged start keeps the output it had; no
+argument used to print this page and exit 2.
+
 Startup prints the loopback URL and private connection-file location, never the
 credential. Opening that URL in a browser on the same machine is the access: the
 service answers a same-origin request from loopback as the local person, with the
@@ -63,7 +79,17 @@ must expire; that link is a credential and is only as good as its five-minute
 window and single use. A credential that is present must still be valid, so an old
 link never silently widens to local access; a same-origin request that carries no
 credential is the machine's own. Host and Origin are checked on every request, and
-a browser request marked as coming from another site is refused. `--port`, `--rscript`, `--core`, `--plugins` and `--limits` are explicit
+a browser request marked as coming from another site is refused.
+
+A start without `--port` takes the port this state's last start had, so a bookmarked
+address and every Agent connection still reach it after a restart; only when another
+program holds that port does it take a new one, and then each Agent connection file in
+the state that named the old address is rewritten to the new one, keeping its token.
+`--port 0` always takes a new port. A selected port that is in use is refused with the
+port named, never replaced. A second start on a state that is already running is
+refused with the running service's address.
+
+`--port`, `--rscript`, `--core`, `--plugins` and `--limits` are explicit
 operator selections; `RHO_RSCRIPT`, `RHO_CORE_BINARY` and `RHO_PYTHON` select
 equivalent runtimes. A Core override is outside bundled digest verification.
 A source checkout has no bundled Core: packaging supplies one per platform under
@@ -106,17 +132,32 @@ Exact Host and supplied Origin are checked. The bearer credential is project
 scoped for external callers. CLI shutdown stops only Hosts started by this
 service and reports confirmation separately. Existing Hosts keep their owner.
 
-### Connect Claude Code
+### Connect Claude Code or Codex
+
+The running service's operator connection adds Rho to the person's own Claude Code
+or Codex for one project, as the project page's "Add to …" button does:
+
+```sh
+rho --grant /absolute/service-state/connection.json --project PROJECT_FOLDER --agent claude-code|codex
+```
+
+It gives that Agent its own grant to the project (kept when it still reaches the
+service), runs that Agent's `mcp remove` and `mcp add` on this machine — Claude Code's
+with `-s local` in the project folder, Codex's for every folder — and records it, so the
+page shows it under that Agent. The JSON reply names the project, its root, the number
+of granted methods, whether a new grant was made, and what was added (`name`, `scope`,
+`at`). A session that was already open does not have the tools; a new one does.
 
-The running service's operator connection grants one project to one Agent session
-and prints how Claude Code starts that session's MCP server:
+Without `--agent`, the same connection grants one project to one Agent session and
+prints how Claude Code starts that session's MCP server:
 
 ```sh
 rho --grant /absolute/service-state/connection.json --project PROJECT_FOLDER [--session NAME]
 ```
 
 `--project` is the folder relative to `--root`; `--session` defaults to
-`claude-code`. The JSON reply names the project, the private session connection
+`claude-code`, the session `--agent claude-code` uses, and `--session codex` is the one
+`--agent codex` uses. When the service is not running, both forms say so and exit 1. The JSON reply names the project, the private session connection
 file, the number of granted methods (the server default), an `mcp` entry
 (`name`, `command`, `args`) for an MCP configuration file, and the equivalent
 `claude mcp add rho-<folder> -- … --mcp <file>` command. `rho --mcp FILE` serves
@@ -155,8 +196,13 @@ configuration stays with Codex (`CODEX_CONFIG` and its native config); Rho does
 copy Claude credentials to Codex. The Westlake acceptance harness supplies an
 isolated native configuration with `tools.update_plan.enabled=true` and
 `features.apply_patch_freeform=true`. This enables real tools, not synthetic plans.
-`maxAgentTurns` is Claude's native step cap; Codex remains bounded by the application
-wall/output/record limits. ACP cancellation confirms the turn, not every native job.
+Rho sets no step cap (`maxAgentTurns`, Claude's `maxTurns`) and no message wall time
+(`turnWallMs`) by default; a `--limits` file can set either under `conversations`. Output,
+line and record limits still apply, and the person can stop a message at any time. A new
+Claude Code session opens in Auto unless the person chose a mode in Rho or their Claude
+settings name one; a model without Auto runs in Accept edits with the adapter's warning.
+Codex's adapter already opens in its own auto-review mode. ACP cancellation confirms the
+turn, not every native job.
 
 For an external ACP client, select this command as that client's Agent executable:
 
@@ -395,7 +441,11 @@ package are absent. Its plugin list must equal the application's runtime selecti
 Production dependencies install with `--omit=optional`, which leaves out only the
 Agent adapters' platform-specific Claude Code and Codex binaries; a native Agent
 client found in the package fails packing, and the installed smoke check fails if
-npm fetched one. Notebook's R and Python runners are its only packed `.R`/`.py`
+npm fetched one. The bundled third-party packages then lose what Node never
+loads: type declarations other than those Rho's own declarations reach, source maps,
+TypeScript sources, tests, examples, documentation and tool configuration. Licenses,
+first-party packages and every file a package names as an entry stay; each file costs
+a Windows installation far more than its bytes. Notebook's R and Python runners are its only packed `.R`/`.py`
 inputs. Each Core's own header (Mach-O, ELF or PE and its machine) must match its
 platform, and the composition records whether a Linux Core is statically linked. Every
 other file is platform-neutral JavaScript: a native Node addon (`.node`) fails packing.
@@ -943,6 +993,11 @@ Notebook 0.1.0 (`@rho-workspace/plugin-kernel`) keeps one live R session and one
 live Python session per project, in the project folder, shared by the person and
 their Agent. `kernel.run` queues a cell in its language's session and starts the
 session when none is live; `waitMs` waits up to `maxWaitMs` for it to end.
+Since Notebook 0.5.3 a cell may name `interpreter`, a program in a folder of the project
+such as an environment's `.venv/bin/python`; the project keeps it for that language's later
+sessions, and a session in which only that caller ran cells starts again with it, while one
+where anyone else ran a cell is refused. Each session and each cell records the program
+(relative to the project when it is in it) and the version that ran it.
 `kernel.read` returns the sessions, their variables and the cells, and never starts
 a session. `kernel.inspect` returns one value of a live session as its session
 describes it: its kind (table, model, vector, list, function, value or other), class,

package/example/pa14-qs/.rho/rho/conversations/c-67f77cfebaba2cea.json

@@ -1 +1 @@
-{"format":2,"backend":"claude-acp","id":"c-67f77cfebaba2cea","changeId":"q-coculture","requestDigest":"61d3c561c68d630b73ad5f0f06b10b60224ee6787f36f52b516d85f3e194b16f","createdAt":"2026-11-01T16:56:09.463Z","createdBy":"browser:local","updatedAt":"2026-11-01T17:15:39.967Z","version":1894,"client":"claude-code","nativeSessionId":null,"confirmed":true,"principal":"agent:0feaa53ea2a60d61f484b80113fd6373","title":"Now the co-culture experiment: when ΔrhlI and ΔlasI are grown together, do they…","turns":[{"id":"t1","changeId":"q-coculture","requestDigest":"61d3c561c68d630b73ad5f0f06b10b60224ee6787f36f52b516d85f3e194b16f","by":"browser:local","text":"Now the co-culture experiment: when ΔrhlI and ΔlasI are grown together, do they swarm like wild type again, and does it depend on the ratio they are mixed at? I care about where the peak is and how strong the ratio effect is. Same rules: R, a figure and a table in results/. One clean figure is enough — do not spend several rounds restyling it.","sentAt":"2026-11-01T16:56:09.463Z","state":"completed","startedAt":"2026-11-01T16:56:09.608Z","endedAt":"2026-11-01T17:11:38.991Z","pid":44481,"model":"westlakehpc/deepseek-v4.1-flash[1m]","stop":null,"exit":null,"steps":[{"kind":"tool","at":"2026-11-01T16:56:18.770Z","id":"chatcmpl-tool-83759658882c8160","tool":"Bash","title":"rtk ls PA14 quorum sensing","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:17.174Z","detail":"rtk ls PA14 quorum sensing","purpose":"List project files","output":{"text":"analysis/\ndata/\nresults/\nREADME.md  1.9K\nproject-notes.md  5.8K","lines":5,"bytes":63,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:18.873Z","id":"chatcmpl-tool-b0cc7a797ff3783e","tool":"Bash","title":"cat PA14 quorum sensing/project-notes.md 2>/dev/null | head -100","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:17.494Z","detail":"cat PA14 quorum sensing/project-notes.md 2>/dev/null | head -100","purpose":"Show existing project notes","output":{"text":"- Used circularity as the primary shape readout and roundness as a check on elongation (the usual reading of these imaging-software metrics; the data sheet does not give their formulas). The two disagree in a useful way: circularity changes strongly while roundness does not, which points to the colony perimeter rather than elongation. See [results/swarming_single_mutants_summary.csv](results/swarming_single_mutants_summary.csv).\n- Added a secondary comparison of rhl mutants against las mutants, pooling the two mutants of each system (6 vs 6 dishes). It is exploratory, not a pre-specified contrast; the per-mutant results show the same ordering. See [results/swarming_system_contrast.csv](results/swarming_system_contrast.csv).\n\n### Files\n\n- [analysis/swarming_single_mutants.R](analysis/swarming_single_mutants.R) — the analysis: data reading, Welch comparisons, assumption checks, sensitivity analyses and the figure; writes the three result files.\n- [results/swarming_single_mutants_summary.csv](results/swarming_single_mutants_summary.csv) — one row per genotype: area, circularity and roundness means and SDs, ratios or differences versus wild type with 95% CIs, and Holm-adjusted p-values.\n- [results/swarming_system_contrast.csv](results/swarming_system_contrast.csv) — rhl mutants versus las mutants for area, circularity and roundness.\n- [results/swarming_single_mutants.png](results/swarming_single_mutants.png) — three-panel figure of area, circularity and roundness by genotype.\n\n### To do\n\n- [x] Explore the swarming data and check distributions\n- [x] Write and run the R analysis\n- [x] Write figure and numeric table to results/","lines":47,"bytes":5903,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:23.713Z","id":"chatcmpl-tool-9c6f61581ee3772e","tool":"Bash","title":"rtk ls PA14 quorum sensing/data PA14 quorum sensing/data/swarming PA14 quorum sensing/results PA14 quorum sensing/analysis 2>/dev/null","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:21.630Z","detail":"rtk ls PA14 quorum sensing/data PA14 quorum sensing/data/swarming PA14 quorum sensing/results PA14 quorum sensing/analysis 2>/dev/null","purpose":"List data, results, analysis directories","output":{"text":"rnaseq/\nswarming/\nswarming_cocultures.R  27.2K\nswarming_single_mutants.R  12.4K\ncocultures.csv  1.8K\nsingle_cultures.csv  612B\nswarming_single_mutants.png  164.1K\nswarming_single_mutants_summary.csv  1.2K\nswarming_system_contrast.csv  302B\n... (4 filtered)","lines":10,"bytes":256,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:25.737Z","id":"chatcmpl-tool-84a44fcec3fa3733","tool":"Bash","title":"cat PA14 quorum sensing/README.md","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:21.983Z","detail":"cat PA14 quorum sensing/README.md","purpose":"Read project README","output":{"text":"\n## Data\n\n| File | What it holds |\n| --- | --- |\n| [data/swarming/single_cultures.csv](data/swarming/single_cultures.csv) | Swarming of wild type and the four single mutants, one dish per row: the colony `area` and `circularity` the imaging software reports, three replicates each. |\n| [data/swarming/cocultures.csv](data/swarming/cocultures.csv) | Swarming of wild type, ΔlasI and ΔrhlI grown alone, and of ΔrhlI:ΔlasI mixes at eleven ratios from 1:3 to 1000:1, three replicates each. `ratio_rhlI_to_lasI` reads ΔrhlI first, so 10:1 is ten ΔrhlI cells per ΔlasI cell. |\n| [data/rnaseq/counts.csv](data/rnaseq/counts.csv) | Raw RNA-seq counts, one row per gene and one column per sample. |\n| [data/rnaseq/samples.csv](data/rnaseq/samples.csv) | What each sample column is: `Media` (MMGluFeMinus, MMGluFePlus, Succinate) × `Strain` (1 wild type, 97 ΔrhlI, 98 ΔlasI, 99 ΔlasIΔrhlI) × `Replicate` (A, B, C). |\n| [data/rnaseq/annotation.csv](data/rnaseq/annotation.csv) | Each locus tag's gene name and product. |\n\nThe data come with the study\n([microPublication Biology, 10.17912/micropub.biology.001326](https://doi.org/10.17912/micropub.biology.001326));\nthe counts and sample sheet are as distributed with it, and the annotation keeps the three\ncolumns this project reads.\n\n## Notes\n\n`area` is in the units the imaging software reports, so it is compared within the assay and\nnever across assays. The swarming assay has three replicates per condition.","lines":29,"bytes":1912,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:35.773Z","id":"chatcmpl-tool-99f6faa46fd24ef8","tool":"Bash","title":"ls -la PA14 quorum sensing/results/ PA14 quorum sensing/analysis/ PA14 quorum sensing/data/swarming/","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:35.090Z","detail":"ls -la PA14 quorum sensing/results/ PA14 quorum sensing/analysis/ PA14 quorum sensing/data/swarming/","purpose":"List directories in full without filtering","output":{"text":"644  swarming_cocultures.R  27.2K\n644  swarming_single_mutants.R  12.4K\n644  cocultures.csv  1.8K\n644  single_cultures.csv  612B\n644  swarming_single_mutants.png  164.1K\n644  swarming_single_mutants_summary.csv  1.2K\n644  swarming_system_contrast.csv  302B\n... (3 filtered)","lines":8,"bytes":273,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:35.802Z","id":"chatcmpl-tool-a1081938778e555d","tool":"Bash","title":"cat PA14 quorum sensing/data/swarming/cocultures.csv","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:35.617Z","detail":"cat PA14 quorum sensing/data/swarming/cocultures.csv","purpose":"Read coculture data","output":{"text":"26,ΔrhlI:ΔlasI,4:1,B,130242,0.065,0.974\n27,ΔrhlI:ΔlasI,4:1,C,189336,0.039,0.964\n28,ΔrhlI:ΔlasI,5:1,A,127082,0.058,0.886\n29,ΔrhlI:ΔlasI,5:1,B,122640,0.069,0.847\n30,ΔrhlI:ΔlasI,5:1,C,104537,0.073,0.965\n31,ΔrhlI:ΔlasI,10:1,A,129141,0.055,0.952\n32,ΔrhlI:ΔlasI,10:1,B,185482,0.038,0.908\n33,ΔrhlI:ΔlasI,10:1,C,238479,0.034,0.971\n34,ΔrhlI:ΔlasI,50:1,A,92265,0.093,0.919\n35,ΔrhlI:ΔlasI,50:1,B,116187,0.066,0.976\n36,ΔrhlI:ΔlasI,50:1,C,73305,0.126,0.734\n37,ΔrhlI:ΔlasI,100:1,A,85812,0.095,0.953\n38,ΔrhlI:ΔlasI,100:1,B,85686,0.095,0.943\n39,ΔrhlI:ΔlasI,100:1,C,51863,0.144,0.624\n40,ΔrhlI:ΔlasI,500:1,A,10623,0.747,0.99\n41,ΔrhlI:ΔlasI,500:1,B,9175,0.856,0.972\n42,ΔrhlI:ΔlasI,500:1,C,10341,0.853,0.8\n43,ΔrhlI:ΔlasI,1000:1,A,14736,0.634,0.834\n44,ΔrhlI:ΔlasI,1000:1,B,73579,0.107,0.977\n45,ΔrhlI:ΔlasI,1000:1,C,47991,0.166,0.99","lines":46,"bytes":1878,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:40.280Z","id":"chatcmpl-tool-abc49b91b018a8de","tool":"Bash","title":"find PA14 quorum sensing -maxdepth 2 -type f | sort; echo ---; cd PA14 quorum sensing && git status --short | head -30; echo ---; git log --oneline -5","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:40.162Z","detail":"find PA14 quorum sensing -maxdepth 2 -type f | sort; echo ---; cd PA14 quorum sensing && git status --short | head -30; echo ---; git log --oneline -5","purpose":"List all files and git state of example project","output":{"text":" M ../../../src/contract.generated.ts\n M ../../../src/conversations.ts\n M ../../../src/protocol.ts\n M ../../../src/server.ts\n M ../../../src/state.ts\n M ../../../web/conversation.tsx\n?? ../../../final4.mjs\n?? ../../../findover.mjs\n?? ../../../narrow.mjs\n?? ../../../overlap.mjs\n?? ../../../shot-artifact.mjs\n?? ../../../shot2.mjs\n?? ../../../shot3.mjs\n?? ../../../shot3all.mjs\n?? ../../../src/example-project.ts---\n7c19d4a4 Record the 0.5.2 candidate for macOS and Linux\nf95906a3 Say why a Core cannot be used instead of printing a stack\n7f0ddc25 Pack one Core per platform and open folders on Linux desktops\na2b752d8 Record the 0.5.2 candidate packed without Agent clients\ne55a7028 Have the doctor say whether Claude Code and Codex are installed","lines":35,"bytes":1702,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:44.577Z","id":"chatcmpl-tool-988897ec9d449ddf","tool":"Read","title":"Read analysis/swarming_cocultures.R","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T16:56:44.547Z","detail":"PA14 quorum sensing/analysis/swarming_cocultures.R"},{"kind":"text","at":"2026-11-01T16:57:31.713Z","id":"msg_resp_bf5f6a4a96777f5b","text":"I'll set up the session notes first, then examine the data and the existing script.\n\n"},{"kind":"tool","at":"2026-11-01T16:57:39.872Z","id":"chatcmpl-tool-b087af16f229c819","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:57:38.173Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T16:57:43.495Z","id":"chatcmpl-tool-8ee84775ea50fe4e","tool":"ToolSearch","title":"ToolSearch","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:57:43.476Z","detail":"select:mcp__rho__rho_index,mcp__rho__rho_resolve,mcp__rho__rho_call,mcp__rho__rho_read"},{"kind":"tool","at":"2026-11-01T16:57:46.402Z","id":"chatcmpl-tool-9758dd4b962f092f","tool":"Bash","title":"Rscript -e 'cat(R.version.string, \"\\n\"); for (p in c(\"dplyr\",\"ggplot2\",\"patchwork\",\"car\")) cat(p, requireNamespace(p, quietly=TRUE), \"\\n\")'","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:57:44.342Z","detail":"Rscript -e 'cat(R.version.string, \"\\n\"); for (p in c(\"dplyr\",\"ggplot2\",\"patchwork\",\"car\")) cat(p, requireNamespace(p, quietly=TRUE), \"\\n\")'","purpose":"Check R version and required packages","output":{"text":"R version 4.5.2 (2025-10-31) \ndplyr TRUE \nggplot2 TRUE \npatchwork TRUE \ncar TRUE","lines":5,"bytes":80,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:57:49.245Z","id":"chatcmpl-tool-8aa652add5b9b56a","tool":"mcp__rho__rho_index","title":"mcp__rho__rho_index","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:57:49.134Z"},{"kind":"tool","at":"2026-11-01T16:57:51.909Z","id":"chatcmpl-tool-b5d7e844d6f9a09c","tool":"Bash","title":"stat -f '%Sm %N' -t '%Y-%m-%d %H:%M' analysis/*.R data/swarming/*.csv results/* project-notes.md","toolKind":"execute","outcome":"rejected","startedAt":"2026-11-01T16:57:50.103Z","detail":"stat -f '%Sm %N' -t '%Y-%m-%d %H:%M' analysis/*.R data/swarming/*.csv results/* project-notes.md","purpose":"Show file modification times","output":{"text":"User refused permission to run tool","lines":1,"bytes":35,"cut":false}},{"kind":"tool","at":"2026-11-01T16:57:54.567Z","id":"chatcmpl-tool-8924b8566aacf77c","tool":"mcp__rho__rho_resolve","title":"mcp__rho__rho_resolve","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:57:53.487Z"},{"kind":"tool","at":"2026-11-01T16:58:06.797Z","id":"chatcmpl-tool-a53c6af8b86531c1","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:04.094Z","operation":"kernel.read"},{"kind":"tool","at":"2026-11-01T16:58:08.750Z","id":"chatcmpl-tool-b6668bdd2a225622","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T16:58:08.690Z","detail":"/sessions"},{"kind":"tool","at":"2026-11-01T16:58:11.740Z","id":"chatcmpl-tool-87aa2178f2f0ce21","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T16:58:11.695Z","detail":"sessions"},{"kind":"tool","at":"2026-11-01T16:58:13.710Z","id":"chatcmpl-tool-b6a231969dc8b6fc","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:13.132Z"},{"kind":"tool","at":"2026-11-01T16:58:15.330Z","id":"chatcmpl-tool-8da822b37ed8843b","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:15.273Z","detail":"/value"},{"kind":"tool","at":"2026-11-01T16:58:21.337Z","id":"chatcmpl-tool-94bc1dff3abc63d1","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:21.282Z","detail":"/value/sessions"},{"kind":"tool","at":"2026-11-01T16:58:26.867Z","id":"chatcmpl-tool-b6f13be6e2f6e28e","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:26.810Z","detail":"/value/cells"},{"kind":"tool","at":"2026-11-01T16:58:29.670Z","id":"chatcmpl-tool-82c643d5496a891a","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:29.608Z","detail":"/value/cells/17"},{"kind":"tool","at":"2026-11-01T16:58:42.837Z","id":"chatcmpl-tool-97fae9de5ea8a4b6","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:42.784Z","detail":"/value/cells/16"},{"kind":"tool","at":"2026-11-01T16:58:42.949Z","id":"chatcmpl-tool-bdffc473b5a743fe","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:42.898Z","detail":"/value/cells/15"},{"kind":"tool","at":"2026-11-01T16:58:49.047Z","id":"chatcmpl-tool-b6df29e2160fba39","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:48.992Z","detail":"/value/cells/14"},{"kind":"tool","at":"2026-11-01T16:58:49.582Z","id":"chatcmpl-tool-a6a7eb5eb8fa3150","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:49.528Z","detail":"/value/cells/13"},{"kind":"tool","at":"2026-11-01T16:58:52.285Z","id":"chatcmpl-tool-beeca28f286edc05","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:52.235Z","detail":"/value/cells/14/outputs"},{"kind":"tool","at":"2026-11-01T16:58:53.691Z","id":"chatcmpl-tool-9a7f20d639074cfb","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:53.631Z","detail":"/value/cells/13/outputs"},{"kind":"tool","at":"2026-11-01T16:58:55.258Z","id":"chatcmpl-tool-84eb28f9f2610671","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:55.206Z","detail":"/value/cells/14/outputs/0/text"},{"kind":"tool","at":"2026-11-01T16:58:58.184Z","id":"chatcmpl-tool-a24d1f1b0e63b5f0","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:58.128Z","detail":"/value/cells/13/outputs/0/text"},{"kind":"text","at":"2026-11-01T17:00:22.995Z","id":"msg_resp_964131adcceda004","text":"The co-culture script was prepared in an earlier, now-ended R session but no results were written. I'll validate its key numbers independently in a fresh live R session, then run it.\n\n"},{"kind":"tool","at":"2026-11-01T17:00:32.445Z","id":"chatcmpl-tool-8dd6945784d8a5e5","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T17:00:23.154Z"},{"kind":"tool","at":"2026-11-01T17:00:44.976Z","id":"chatcmpl-tool-9bffba28deeac9f8","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:00:43.645Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:01:07.429Z","id":"chatcmpl-tool-92c90b4ce3d359a6","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:01:02.388Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:01:31.512Z","id":"chatcmpl-tool-8d498cdb0c2fbca7","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:01:13.614Z","operation":"kernel.run"},{"kind":"text","at":"2026-11-01T17:02:15.931Z","id":"msg_resp_b0a84a4ae7152853","text":"Independent checks reproduce the prepared model: peak 12.3:1 (bootstrap 95% CI 10.4–14.7), quadratic R² 0.89, one-way ratio R² 0.93. Now I'll run the full script to write the result files and figure.\n\n"},{"kind":"tool","at":"2026-11-01T17:02:19.472Z","id":"chatcmpl-tool-83e899c6387d50f5","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:02:15.932Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:02:33.917Z","id":"chatcmpl-tool-80d6d7cb2533b591","tool":"Read","title":"Read results/swarming_cocultures_summary.csv","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:02:33.896Z","detail":"PA14 quorum sensing/results/swarming_cocultures_summary.csv"},{"kind":"tool","at":"2026-11-01T17:02:34.332Z","id":"chatcmpl-tool-b0f6d7b0f487660b","tool":"Read","title":"Read results/swarming_cocultures_ratio_model.csv","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:02:34.314Z","detail":"PA14 quorum sensing/results/swarming_cocultures_ratio_model.csv"},{"kind":"tool","at":"2026-11-01T17:02:36.333Z","id":"chatcmpl-tool-8f2ec59002d4b779","tool":"Read","title":"Read results/swarming_cocultures.png","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:02:36.180Z","detail":"PA14 quorum sensing/results/swarming_cocultures.png"},{"kind":"text","at":"2026-11-01T17:04:15.829Z","id":"msg_resp_9c4f255399978a20","text":"The script wrote all three result files. Before writing the findings, I'll check one interpretive point: whether the fitted peak is distinguishable from wild type once wild-type dish variability is included, and the overall ratio ANOVA.\n\n\n\n"},{"kind":"tool","at":"2026-11-01T17:04:21.776Z","id":"chatcmpl-tool-a7717366a2c3d402","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:04:15.829Z","operation":"kernel.run"},{"kind":"text","at":"2026-11-01T17:04:58.630Z","id":"msg_resp_aa538e63bf0d58d0","text":"The peak-to-wild-type bootstrap (resampling both mix and wild-type dishes) gives 0.99–1.70, so the peak is statistically indistinguishable from wild type. That belongs in the result table, so I'll add it and the one-way ratio p-value to the script, then re-run.\n\n"},{"kind":"tool","at":"2026-11-01T17:05:06.774Z","id":"chatcmpl-tool-b67503b704a95a97","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:04.844Z","detail":"PA14 quorum sensing/analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:12.806Z","id":"chatcmpl-tool-a1e0e2d1aa7e465f","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:11.743Z","detail":"PA14 quorum sensing/analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:18.841Z","id":"chatcmpl-tool-ae8cdd54746f8082","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:16.847Z","detail":"PA14 quorum sensing/analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:24.863Z","id":"chatcmpl-tool-a6d1b3c2dfab27cd","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:23.179Z","detail":"PA14 quorum sensing/analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:30.901Z","id":"chatcmpl-tool-b25c09ec1e9ffc25","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:30.036Z","detail":"PA14 quorum sensing/analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:38.426Z","id":"chatcmpl-tool-b8151231bba7b10e","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:05:33.364Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:05:43.005Z","id":"chatcmpl-tool-8d7ce51e52a0c488","tool":"Bash","title":"grep -n 'peak_over_wildtype\\|ratio_one_way_p\\|one_way_p' results/swarming_cocultures_ratio_model.csv; echo ---; ls -l results/","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T17:05:41.979Z","detail":"grep -n 'peak_over_wildtype\\|ratio_one_way_p\\|one_way_p' results/swarming_cocultures_ratio_model.csv; echo ---; ls -l results/","purpose":"Check new model rows and result files","output":{"text":"9:\"area\",\"ratio_one_way_p\",1.23629e-09,NA,NA,\"one-way ANOVA F test across the 10 window ratios\"\n12:\"area\",\"peak_over_wildtype\",1.34221,0.989285,1.71213,\"fitted peak geometric mean / wild-type geometric mean; bootstrap 95% CI resampling mix and wild-type dishes\"\n---\n644  swarming_cocultures.png  228.6K\n644  swarming_cocultures_ratio_model.csv  4.2K\n644  swarming_cocultures_summary.csv  3.3K\n644  swarming_single_mutants.png  164.1K\n644  swarming_single_mutants_summary.csv  1.2K\n644  swarming_system_contrast.csv  302B","lines":9,"bytes":520,"cut":false},"exitCode":0},{"kind":"text","at":"2026-11-01T17:06:31.254Z","id":"msg_resp_a338e57a36af850f","text":"All result files are in place. Now I'll write the findings into the session notes.\n\n"},{"kind":"tool","at":"2026-11-01T17:06:33.198Z","id":"chatcmpl-tool-a31f6867366b5a60","tool":"Read","title":"Read project-notes.md (from line 55)","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:06:33.178Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:09.093Z","id":"chatcmpl-tool-afa93163df2807bd","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:07.826Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:13.784Z","id":"chatcmpl-tool-91469059f68c4d4a","tool":"Read","title":"Read project-notes.md (from line 48)","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:07:13.765Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:33.151Z","id":"chatcmpl-tool-98f42ffae1befa60","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:31.670Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:35.182Z","id":"chatcmpl-tool-a549f5938b4d60ee","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:33.141Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:37.204Z","id":"chatcmpl-tool-87ae6a2c21aa0238","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:34.781Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:08:17.319Z","id":"chatcmpl-tool-8cb7dc915ddc4fa2","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:08:15.832Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T17:10:19.593Z","id":"chatcmpl-tool-8de2edd619034840","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:10:18.645Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"text","at":"2026-11-01T17:10:41.443Z","id":"msg_resp_ba1d3c9f48ea6588","text":"The notes are updated. One last check: run the saved script standalone with `Rscript` to confirm the results reproduce without the live session.\n\n"},{"kind":"tool","at":"2026-11-01T17:10:47.974Z","id":"chatcmpl-tool-beb256a58642eedc","tool":"Bash","title":"Rscript analysis/swarming_cocultures.R 2>&1 | tail -25","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T17:10:42.754Z","detail":"Rscript analysis/swarming_cocultures.R 2>&1 | tail -25","purpose":"Run the co-culture analysis script standalone","output":{"text":"Multiple R-squared:  0.8908,\tAdjusted R-squared:  0.8827 \nF-statistic: 110.2 on 2 and 27 DF,  p-value: 1.034e-13\n\nPeak ratio: 12.27 :1  95% CI 10.4-14.67 \nPeak area: 145880  95% CI 132127-161011 \nPeak / wild type: 1.34  95% CI 0.99-1.71 \nWild-type geometric mean: 108686 \nFitted area reaches the wild-type mean between ratios 3.24 and 46.4 \nOne-way ratio R2: 0.93  quadratic R2: 0.891 \nSensitivity peaks: all 12 = 15.63 ; excl 1000:1 = 11.16 ; excl 500:1 = 22.36 \nLeave-one-ratio-out peaks: 12.32 12.28 11.89 12.2 11.9 12.81 12.12 12.41 13.05 11.62 \n\nCircularity minimum at 12.22 :1; fitted 0.05 vs wild type 0.061 \nRoundness fitted maximum at 12.17 :1; fitted 0.97 vs wild type 0.855 \n\nAssumption checks: Levene p = 0.939 ; Shapiro p = 0.666 ; max Cook's D = 0.184 \n\nWrote results/swarming_cocultures_summary.csv\nWrote results/swarming_cocultures_ratio_model.csv\nWrote results/swarming_cocultures.png","lines":25,"bytes":1100,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T17:10:54.635Z","id":"chatcmpl-tool-8c51cf1fcd7e00fc","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:10:54.077Z"},{"kind":"text","at":"2026-11-01T17:11:38.970Z","id":"msg_resp_9af7b0624738af67","text":"Yes — co-culture restores swarming, and the ratio matters strongly.\n\n**Peak.** The fitted optimum is **12.3:1 ΔrhlI:ΔlasI** (cluster-bootstrap 95% CI **10.4–14.7:1**). At the peak, fitted area is **145,880** versus a wild-type geometric mean of **108,686** — **1.34× wild type** (95% CI **0.99–1.71**). The nearest observed mix, 10:1, was 1.64× wild type (0.83–3.25, unadjusted p = 0.11), so the peak is statistically indistinguishable from wild type, not significantly above it. For comparison, ΔrhlI alone was 0.094× and ΔlasI alone 0.134× wild type, so the peak is about 14× and 10× their own areas.\n\n**Ratio effect.** Across the ten well-sampled ratios (1:3–100:1), the mixing ratio explains **93% of the variance in log area** (one-way ANOVA F(9,20) = 29.5, p = 1.2 × 10⁻⁹; quadratic R² = 0.891 versus 0.364 for a linear fit). The fitted peak is **8.7×** the 1:3 value, **2.1×** the 100:1 value and **14.5×** the 500:1 value. Fitted area reaches wild-type level between **3.2:1 and 46.4:1**. Beyond that, rescue collapses at 500:1 (0.09× wild type, the only mix significantly below wild type after Holm, p = 0.037) and is heterogeneous at 1000:1 (0.34×, CI 0.06–2.14). Shape converges on the same optimum: circularity reaches its minimum at 12.2:1 and roundness its maximum at 12.2:1.\n\n**Caveats.** Three dishes per condition; the low-ratio pairwise reductions (0.17–0.39× wild type) are only borderline after Holm correction (p = 0.073–0.121), so the overall model carries that part of the conclusion. The peak location depends on the fitted window: including all twelve ratios gives 15.6:1 but a poor fit (R² 0.66), while excluding only 500:1 or only 1000:1 gives 22.4:1 or 11.2:1. Within the observed rescue window, leave-one-ratio-out peaks span 11.6–13.1.\n\nFiles:\n- [analysis/swarming_cocultures.R](analysis/swarming_cocultures.R) — full analysis, reproduces everything with `Rscript analysis/swarming_cocultures.R`\n- [results/swarming_cocultures_summary.csv](results/swarming_cocultures_summary.csv) — per-condition table with comparisons versus wild type\n- [results/swarming_cocultures_ratio_model.csv](results/swarming_cocultures_ratio_model.csv) — peak, ratio effect, sensitivity and diagnostic table\n- [results/swarming_cocultures.png](results/swarming_cocultures.png) — one three-panel figure (area, circularity, roundness)\n\nThe shared notes are updated in [project-notes.md](project-notes.md)."}],"omitted":0,"retry":null,"result":{"isError":false,"kind":"acp","reason":"end_turn","steps":null,"durationMs":929384,"costUsd":null,"message":null},"problem":null,"evidence":{"records":[{"key":"command:chatcmpl-tool-b0cc7a797ff3783e:undefined:project-notes.md","path":"project-notes.md","phase":"command:chatcmpl-tool-b0cc7a797ff3783e:undefined","requestedAt":"2026-11-01T16:56:17.386Z","state":"captured","snapshots":[{"resource":{"id":"9678539599c516fbc3e2d54614d7f89b299ca0edf9fae04c8eb053c7cdac21c2","version":"03bd35607b650b6c13336489c010d620a4e1a7e7204042cbf10fa47ac77af97a"},"kind":"file","bytes":5904,"observedAt":"2026-11-01T16:56:17.421Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"command:chatcmpl-tool-84a44fcec3fa3733:undefined:README.md","path":"README.md","phase":"command:chatcmpl-tool-84a44fcec3fa3733:undefined","requestedAt":"2026-11-01T16:56:21.798Z","state":"captured","snapshots":[{"resource":{"id":"8335a7f50594c96793bc5243e62e561d84b542c23802378deb7c8907fc467447","version":"56924e744562b67c05bb53bad2914c31ed4997eb1e7c7ef6e58e37080e049d09"},"kind":"file","bytes":1913,"observedAt":"2026-11-01T16:56:21.837Z","source":{"kind":"disk","path":"README.md"}}]},{"key":"command:chatcmpl-tool-a1081938778e555d:undefined:data/swarming/cocultures.csv","path":"data/swarming/cocultures.csv","phase":"command:chatcmpl-tool-a1081938778e555d:undefined","requestedAt":"2026-11-01T16:56:35.360Z","state":"captured","snapshots":[{"resource":{"id":"2877ce204ee89e35151335d1be02c23e13b79868f8fb9d12969178265b6450eb","version":"b1b12af73ab2e4ce4a19a2295a85cb485241c1223dd71ef54313a0c206c87a33"},"kind":"table","bytes":1879,"observedAt":"2026-11-01T16:56:35.407Z","source":{"kind":"disk","path":"data/swarming/cocultures.csv"}}]},{"key":"tool:chatcmpl-tool-988897ec9d449ddf:requested:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-988897ec9d449ddf:requested","requestedAt":"2026-11-01T16:56:44.547Z","state":"captured","snapshots":[{"resource":{"id":"1f1eb2c001a34e511db6575708978dfd54e8fbe20fd21dfc5742da12781da6cf","version":"7c473232d1a129f4ebb7704a20a67aa6088eb55c1ad1d0dd90f37c36251630f1"},"kind":"file","bytes":27885,"observedAt":"2026-11-01T16:56:44.582Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-b087af16f229c819:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-b087af16f229c819:returned","requestedAt":"2026-11-01T16:57:39.872Z","state":"captured","snapshots":[{"resource":{"id":"66512b5f72c9ac74714c2c3b55975d8eab987d49d216739e2c2d53be7ab707be","version":"bca642094971b5fe7769377a249d2587e79980c8043cdcc9d9f19e3403d8ad23"},"kind":"file","bytes":7306,"observedAt":"2026-11-01T16:57:39.926Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-80d6d7cb2533b591:requested:results/swarming_cocultures_summary.csv","path":"results/swarming_cocultures_summary.csv","phase":"tool:chatcmpl-tool-80d6d7cb2533b591:requested","requestedAt":"2026-11-01T17:02:33.896Z","state":"captured","snapshots":[{"resource":{"id":"dbec0f2c3a8daf9012a5ca95678df3e70b06bcd37edf5ab79c6b265301b2e91b","version":"2519bcb743fdede4abbe09cefa70a761d3276ea00ecfb200a3f2a7c7a1580381"},"kind":"table","bytes":3407,"observedAt":"2026-11-01T17:02:33.933Z","source":{"kind":"disk","path":"results/swarming_cocultures_summary.csv"}}]},{"key":"tool:chatcmpl-tool-b0f6d7b0f487660b:requested:results/swarming_cocultures_ratio_model.csv","path":"results/swarming_cocultures_ratio_model.csv","phase":"tool:chatcmpl-tool-b0f6d7b0f487660b:requested","requestedAt":"2026-11-01T17:02:34.314Z","state":"captured","snapshots":[{"resource":{"id":"d9cd275ad886225d1f115731a20522998ab16f59c44b1d519cfa42cb764570b7","version":"9b46e669452e972f12f49ab47f64daa571d8d1a3b80a591f9028105feb2a8d10"},"kind":"table","bytes":4157,"observedAt":"2026-11-01T17:02:34.350Z","source":{"kind":"disk","path":"results/swarming_cocultures_ratio_model.csv"}}]},{"key":"tool:chatcmpl-tool-8f2ec59002d4b779:requested:results/swarming_cocultures.png","path":"results/swarming_cocultures.png","phase":"tool:chatcmpl-tool-8f2ec59002d4b779:requested","requestedAt":"2026-11-01T17:02:36.180Z","state":"captured","snapshots":[{"resource":{"id":"cc393e70db0c4ff8d76b62db44f8de288d42af35fa2d537dabf0c49557c1c6a8","version":"94aafdb53e5916fb35ca0eaf7c403ff822c907bf43fed39188772e103cf9c8c6"},"kind":"media","bytes":234096,"observedAt":"2026-11-01T17:02:36.221Z","source":{"kind":"disk","path":"results/swarming_cocultures.png"}}]},{"key":"tool:chatcmpl-tool-b67503b704a95a97:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-b67503b704a95a97:returned","requestedAt":"2026-11-01T17:05:06.774Z","state":"captured","snapshots":[{"resource":{"id":"880bbf79eb2efd54457926608541939342bd6d6457b8dff56e36a64f9d700202","version":"a0641d022a11af6400a9f19a963eccb2ae464fce6c23752360807181ae667df5"},"kind":"file","bytes":28495,"observedAt":"2026-11-01T17:05:06.833Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-a1e0e2d1aa7e465f:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-a1e0e2d1aa7e465f:returned","requestedAt":"2026-11-01T17:05:12.806Z","state":"captured","snapshots":[{"resource":{"id":"e24daf11fe7991c0bb5518b72a217661b2f24b2fe593aeaed0949d5b37cc4717","version":"633d6a61c2263a8be8d5b39b0763613778c20bf41851b5cb37c0e0e57468da2d"},"kind":"file","bytes":28626,"observedAt":"2026-11-01T17:05:12.868Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-ae8cdd54746f8082:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-ae8cdd54746f8082:returned","requestedAt":"2026-11-01T17:05:18.841Z","state":"captured","snapshots":[{"resource":{"id":"4ce0a7aac07e36c2dda77f16fee4ca0db2f66ea0823b8ac1d892f2b30ff43b73","version":"6d0d380b56cccc5f0dbb7e5e6a051b9b9c898b28f055a9e4df130b1f2fa7bcca"},"kind":"file","bytes":28758,"observedAt":"2026-11-01T17:05:18.904Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-a6d1b3c2dfab27cd:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-a6d1b3c2dfab27cd:returned","requestedAt":"2026-11-01T17:05:24.863Z","state":"captured","snapshots":[{"resource":{"id":"4a2f3f58108ffb842da662a571675120e444a7897f2b064df478ae53e56293bf","version":"d5955e8b61fa45349533a9ad2432ee7da065ea20702781d83decdfd4eea68577"},"kind":"file","bytes":28849,"observedAt":"2026-11-01T17:05:24.923Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-b25c09ec1e9ffc25:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-b25c09ec1e9ffc25:returned","requestedAt":"2026-11-01T17:05:30.901Z","state":"captured","snapshots":[{"resource":{"id":"c1d7ec4d732037c1aec395abc8a8d6b2845acdcd8f91954936e0245cf7181137","version":"553390f7520a6266c4f2b72a4df9e450b5383ddb4ab1ed4f9a17076e7b43bde7"},"kind":"file","bytes":28974,"observedAt":"2026-11-01T17:05:30.962Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"command:chatcmpl-tool-8d7ce51e52a0c488:undefined:results/swarming_cocultures_ratio_model.csv","path":"results/swarming_cocultures_ratio_model.csv","phase":"command:chatcmpl-tool-8d7ce51e52a0c488:undefined","requestedAt":"2026-11-01T17:05:41.471Z","state":"captured","snapshots":[{"resource":{"id":"51ac10dda0efe4248cec3eadb2292ca6ffaebe1a3ba7e11352a18ddcb94aa26b","version":"6ea552f15c636fe63addf0ca67c93a4a8cc866a7699e925ca9fe112f5b7a4123"},"kind":"table","bytes":4316,"observedAt":"2026-11-01T17:05:41.529Z","source":{"kind":"disk","path":"results/swarming_cocultures_ratio_model.csv"}}]},{"key":"tool:chatcmpl-tool-afa93163df2807bd:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-afa93163df2807bd:returned","requestedAt":"2026-11-01T17:07:09.093Z","state":"captured","snapshots":[{"resource":{"id":"fdc072913da27e66864b86609b041dec9f83c2ab5b3a045c5c9961f51b75cd49","version":"36ce157e29eb6299bf44523078bdc3e3c9422fc541a31b030609fc3571d593d4"},"kind":"file","bytes":13145,"observedAt":"2026-11-01T17:07:09.151Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-98f42ffae1befa60:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-98f42ffae1befa60:returned","requestedAt":"2026-11-01T17:07:33.151Z","state":"captured","snapshots":[{"resource":{"id":"5bcbcb5366e1246d6546d77758c8bbeefc92354129bb3f62d56638bb55f31c50","version":"3f0337a2e0b2bca1b2c1f97b5d5a385f3e6f3997cb6ec135e3338ceb41a86a11"},"kind":"file","bytes":13155,"observedAt":"2026-11-01T17:07:33.209Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-a549f5938b4d60ee:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-a549f5938b4d60ee:returned","requestedAt":"2026-11-01T17:07:35.182Z","state":"captured","snapshots":[{"resource":{"id":"ac7c3acef2c511ab3276071f1d4f8c78633755a57254471c7266cbe361437411","version":"8fad929a7edd138583741fadec37e1bdc995ee7644416dabc7c0d8573d2c5f50"},"kind":"file","bytes":13295,"observedAt":"2026-11-01T17:07:35.239Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-87ae6a2c21aa0238:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-87ae6a2c21aa0238:returned","requestedAt":"2026-11-01T17:07:37.204Z","state":"captured","snapshots":[{"resource":{"id":"de430b43443f9cde4a9a69a3467f662eaf3c264e1a788ea61212de27e5909cd3","version":"22ff16a058c9fd5a787d8376812fba2ca0a160717649bf2a38165ab0f044a307"},"kind":"file","bytes":13307,"observedAt":"2026-11-01T17:07:37.264Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-8cb7dc915ddc4fa2:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-8cb7dc915ddc4fa2:returned","requestedAt":"2026-11-01T17:08:17.319Z","state":"captured","snapshots":[{"resource":{"id":"fbfba969896f136f9e82eccd97ebdbef67a399243fe4d49c217719fb98108aef","version":"c2d5bb55680c49cb7c6f438bc5e7f32ab4989861632558dfde516a2bdce4148b"},"kind":"file","bytes":13402,"observedAt":"2026-11-01T17:08:17.378Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-8de2edd619034840:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-8de2edd619034840:returned","requestedAt":"2026-11-01T17:10:19.593Z","state":"captured","snapshots":[{"resource":{"id":"690166e11c1aa3994bc335f77a69278dbf7360b501ec69334de3998f50df6b91","version":"00c5e3db1d1cc3fa0bf4e4951d7df99f17cd4d2d950feb1ba96080a1f726ebb2"},"kind":"file","bytes":13424,"observedAt":"2026-11-01T17:10:19.653Z","source":{"kind":"disk","path":"project-notes.md"}}]}],"omitted":0,"bytes":514293,"snapshots":20},"permissions":[{"id":"aa6968bd-8c81-4c0c-902c-a30220ccf28e","toolCallId":"chatcmpl-tool-83759658882c8160","title":"rtk ls PA14 quorum sensing","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"90fcef40-17b5-4738-a12c-4b08687e6841","toolCallId":"chatcmpl-tool-9c6f61581ee3772e","title":"rtk ls PA14 quorum sensing/data PA14 quorum sensing/data/swarming PA14 quorum sensing/results PA14 quorum sensing/analysis 2>/dev/null","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"f31a0786-283a-4833-aad4-4cde72c9d49e","toolCallId":"chatcmpl-tool-84a44fcec3fa3733","title":"rtk read PA14 quorum sensing/README.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk read * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"ae84eda5-e523-483c-9558-a057b4235733","toolCallId":"chatcmpl-tool-99f6faa46fd24ef8","title":"rtk ls -la PA14 quorum sensing/results/ PA14 quorum sensing/analysis/ PA14 quorum sensing/data/swarming/","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"be0299de-e2f0-4d4a-83b4-9d821fe37ac6","toolCallId":"chatcmpl-tool-a1081938778e555d","title":"rtk read PA14 quorum sensing/data/swarming/cocultures.csv","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk read * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"24aaaf41-798f-4169-9165-f1589435476b","toolCallId":"chatcmpl-tool-b087af16f229c819","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"dae866e8-3f89-4d1c-80df-f51f7f436068","toolCallId":"chatcmpl-tool-9758dd4b962f092f","title":"Rscript -e 'cat(R.version.string, \"\\n\"); for (p in c(\"dplyr\",\"ggplot2\",\"patchwork\",\"car\")) cat(p, requireNamespace(p, quietly=TRUE), \"\\n\")'","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for similar commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"e0ff4efd-9ea4-4141-8a50-a08ed357caa7","toolCallId":"chatcmpl-tool-b5d7e844d6f9a09c","title":"rtk stat -f '%Sm %N' -t '%Y-%m-%d %H:%M' analysis/*.R data/swarming/*.csv results/* project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk stat * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"reject"},{"id":"355b5915-4edb-4790-8536-70764f3bab60","toolCallId":"chatcmpl-tool-b67503b704a95a97","title":"Edit analysis/swarming_cocultures.R","details":"PA14 quorum sensing/analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"5f055788-9ea1-4451-8f80-204a47757afe","toolCallId":"chatcmpl-tool-a1e0e2d1aa7e465f","title":"Edit analysis/swarming_cocultures.R","details":"PA14 quorum sensing/analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"ea7fb496-310b-4da6-bcbd-73c76ca1003c","toolCallId":"chatcmpl-tool-ae8cdd54746f8082","title":"Edit analysis/swarming_cocultures.R","details":"PA14 quorum sensing/analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"422738dc-8dfb-48a2-bb67-938bf3625411","toolCallId":"chatcmpl-tool-a6d1b3c2dfab27cd","title":"Edit analysis/swarming_cocultures.R","details":"PA14 quorum sensing/analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"edecd14a-de2d-4345-9cbc-3d908ecc4f82","toolCallId":"chatcmpl-tool-b25c09ec1e9ffc25","title":"Edit analysis/swarming_cocultures.R","details":"PA14 quorum sensing/analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"195ad4a2-399a-4641-8918-9e813a7f823a","toolCallId":"chatcmpl-tool-8d7ce51e52a0c488","title":"rtk grep -n 'peak_over_wildtype\\|ratio_one_way_p\\|one_way_p' results/swarming_cocultures_ratio_model.csv; echo ---; rtk ls -l results/","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk grep * and rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"df8d54e0-f89a-4365-a612-43e8994f8a91","toolCallId":"chatcmpl-tool-afa93163df2807bd","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"34b82c68-1a55-49aa-abd2-44bde9e880f4","toolCallId":"chatcmpl-tool-98f42ffae1befa60","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"b65597d3-cdb2-433a-a4a8-160a1c44215f","toolCallId":"chatcmpl-tool-a549f5938b4d60ee","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"6237174f-5679-4e17-b0b7-06c1f0d61cf3","toolCallId":"chatcmpl-tool-87ae6a2c21aa0238","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"5259caf8-47d4-418f-810d-3825868d0428","toolCallId":"chatcmpl-tool-8cb7dc915ddc4fa2","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"4f2e957c-9639-4868-8e83-2e7a10450f53","toolCallId":"chatcmpl-tool-8de2edd619034840","title":"Edit project-notes.md","details":"PA14 quorum sensing/project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"a7418516-ca89-4a01-8732-077f8b06a08c","toolCallId":"chatcmpl-tool-beb256a58642eedc","title":"Rscript analysis/swarming_cocultures.R 2>&1 | tail -25","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for Rscript analysis/swarming_cocultures.R commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"}],"descriptions":[{"path":"results/swarming_cocultures_summary.csv","version":"2519bcb743fdede4abbe09cefa70a761d3276ea00ecfb200a3f2a7c7a1580381","bytes":3407,"modifiedAt":"2026-11-01T17:10:44.180Z","observedAt":"2026-11-01T17:02:19.667Z","facts":"15 rows × 25 columns: condition, culture, ratio_rhlI_to_lasI, ratio_numeric, n, area_mean, area_sd, area_geomean, … (17 more)","sentence":{"text":"The summary CSV holds 15 co-culture rows and 25 columns, covering wild type, single mutants, and ΔrhlI:ΔlasI mixes from 1:3 to 1000:1, with area, circularity, and roundness statistics.","version":"2519bcb743fdede4abbe09cefa70a761d3276ea00ecfb200a3f2a7c7a1580381","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:02:25.376Z","facts":"15 rows × 25 columns: condition, culture, ratio_rhlI_to_lasI, ratio_numeric, n, area_mean, area_sd, area_geomean, … (17 more)","strategy":"text","cost":{"usd":0.0007769341439999999,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"},{"path":"results/swarming_cocultures_ratio_model.csv","version":"6ea552f15c636fe63addf0ca67c93a4a8cc866a7699e925ca9fe112f5b7a4123","bytes":4316,"modifiedAt":"2026-11-01T17:10:47.403Z","observedAt":"2026-11-01T17:05:44.704Z","facts":"50 rows × 6 columns: metric, quantity, estimate, ci_low, ci_high, detail","sentence":{"text":"This CSV holds 50 rows of co-culture ratio-model results, with columns metric, quantity, estimate, confidence bounds and detail, covering area and circularity fits.","version":"6ea552f15c636fe63addf0ca67c93a4a8cc866a7699e925ca9fe112f5b7a4123","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:05:48.580Z","facts":"50 rows × 6 columns: metric, quantity, estimate, ci_low, ci_high, detail","strategy":"text","cost":{"usd":0.000576200832,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"},{"path":"results/swarming_cocultures.png","version":"94aafdb53e5916fb35ca0eaf7c403ff822c907bf43fed39188772e103cf9c8c6","bytes":234096,"modifiedAt":"2026-11-01T17:10:47.942Z","observedAt":"2026-11-01T17:02:24.666Z","facts":"PNG image, 2760 × 1380 px, 228.6 KB","sentence":{"text":"Three scatter panels plot colony area (log scale), circularity and roundness against ΔrhlI:ΔlasI mix ratio, comparing mix points and fitted curves to Wild type, ΔlasI alone and ΔrhlI alone lines.","version":"94aafdb53e5916fb35ca0eaf7c403ff822c907bf43fed39188772e103cf9c8c6","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:02:37.561Z","facts":"PNG image, 2760 × 1380 px, 228.6 KB","strategy":"image","cost":{"usd":0.000921571776,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"},{"path":"analysis/swarming_cocultures.R","version":"553390f7520a6266c4f2b72a4df9e450b5383ddb4ab1ed4f9a17076e7b43bde7","bytes":28974,"modifiedAt":"2026-11-01T17:05:30.881Z","observedAt":"2026-11-01T17:05:34.702Z","facts":"R script, 669 lines, 11 functions","sentence":{"text":"An R script analyzing ΔrhlI/ΔlasI co-culture swarming across twelve mix ratios, comparing each to wild type and fitting a quadratic ratio model, writing two results CSVs and a three-panel figure.","version":"553390f7520a6266c4f2b72a4df9e450b5383ddb4ab1ed4f9a17076e7b43bde7","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:06:12.932Z","facts":"R script, 669 lines, 11 functions","strategy":"text","cost":{"usd":0.00046038969599999994,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"}],"descriptionSpend":{"calls":6,"usd":0.003848802816,"estimated":6,"unknown":0},"files":{"changed":[{"path":"analysis/swarming_cocultures.R","change":"modified","modifiedAt":"2026-11-01T17:05:30.881Z","bytes":28974},{"path":"project-notes.md","change":"modified","modifiedAt":"2026-11-01T17:10:19.578Z","bytes":13424},{"path":"results/swarming_cocultures_summary.csv","change":"added","modifiedAt":"2026-11-01T17:10:44.180Z","bytes":3407},{"path":"results/swarming_cocultures_ratio_model.csv","change":"added","modifiedAt":"2026-11-01T17:10:47.403Z","bytes":4316},{"path":"results/swarming_cocultures.png","change":"added","modifiedAt":"2026-11-01T17:10:47.942Z","bytes":234096}],"omitted":0,"partial":false}}],"config":{"model":"westlakehpc/deepseek-v4.1-flash[1m]"},"acpSessionId":"eb7e3d77-aaa1-464b-be54-4b9b5b9cf987","protocolVersion":1,"adapter":{"name":"@agentclientprotocol/claude-agent-acp","version":"0.97.0"},"model":"westlakehpc/deepseek-v4.1-flash[1m]","observation":{"source":"acp","sessionId":"eb7e3d77-aaa1-464b-be54-4b9b5b9cf987","sequence":11724,"at":"2026-11-01T17:15:39.634Z","connected":false,"updates":11721,"historyUpdates":0,"omitted":24,"unrepresented":11016,"plan":null,"usage":{"at":"2026-11-01T17:11:38.990Z","origin":"live","used":127830,"size":1000000,"cost":{"amount":3.568275999999999,"currency":"USD"}},"info":null,"tools":[{"at":"2026-11-01T16:58:49.046Z","origin":"live","id":"chatcmpl-tool-b6df29e2160fba39","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:49.582Z","origin":"live","id":"chatcmpl-tool-a6a7eb5eb8fa3150","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:52.285Z","origin":"live","id":"chatcmpl-tool-beeca28f286edc05","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:53.691Z","origin":"live","id":"chatcmpl-tool-9a7f20d639074cfb","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:55.258Z","origin":"live","id":"chatcmpl-tool-84eb28f9f2610671","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:58.183Z","origin":"live","id":"chatcmpl-tool-a24d1f1b0e63b5f0","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T17:00:32.445Z","origin":"live","id":"chatcmpl-tool-8dd6945784d8a5e5","locations":[],"tool":"mcp__rho__rho_call","outcome":"rejected"},{"at":"2026-11-01T17:00:44.975Z","origin":"live","id":"chatcmpl-tool-9bffba28deeac9f8","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:01:07.428Z","origin":"live","id":"chatcmpl-tool-92c90b4ce3d359a6","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:01:31.511Z","origin":"live","id":"chatcmpl-tool-8d498cdb0c2fbca7","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:02:19.472Z","origin":"live","id":"chatcmpl-tool-83e899c6387d50f5","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:02:33.917Z","origin":"live","id":"chatcmpl-tool-80d6d7cb2533b591","locations":[{"path":"PA14 quorum sensing/results/swarming_cocultures_summary.csv","line":1}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:02:34.332Z","origin":"live","id":"chatcmpl-tool-b0f6d7b0f487660b","locations":[{"path":"PA14 quorum sensing/results/swarming_cocultures_ratio_model.csv","line":1}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:02:36.332Z","origin":"live","id":"chatcmpl-tool-8f2ec59002d4b779","locations":[{"path":"PA14 quorum sensing/results/swarming_cocultures.png","line":1}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:04:21.776Z","origin":"live","id":"chatcmpl-tool-a7717366a2c3d402","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:05:06.773Z","origin":"live","id":"chatcmpl-tool-b67503b704a95a97","locations":[{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R","line":257},{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:12.806Z","origin":"live","id":"chatcmpl-tool-a1e0e2d1aa7e465f","locations":[{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R","line":292},{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:18.841Z","origin":"live","id":"chatcmpl-tool-ae8cdd54746f8082","locations":[{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R","line":364},{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:24.863Z","origin":"live","id":"chatcmpl-tool-a6d1b3c2dfab27cd","locations":[{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R","line":371},{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:30.901Z","origin":"live","id":"chatcmpl-tool-b25c09ec1e9ffc25","locations":[{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R","line":475},{"path":"PA14 quorum sensing/analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:38.426Z","origin":"live","id":"chatcmpl-tool-b8151231bba7b10e","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:05:43.004Z","origin":"live","id":"chatcmpl-tool-8d7ce51e52a0c488","locations":[],"tool":"Bash","outcome":"returned"},{"at":"2026-11-01T17:06:33.198Z","origin":"live","id":"chatcmpl-tool-a31f6867366b5a60","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":55}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:07:09.092Z","origin":"live","id":"chatcmpl-tool-afa93163df2807bd","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":59},{"path":"PA14 quorum sensing/project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:07:13.784Z","origin":"live","id":"chatcmpl-tool-91469059f68c4d4a","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":48}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:07:33.151Z","origin":"live","id":"chatcmpl-tool-98f42ffae1befa60","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":64},{"path":"PA14 quorum sensing/project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:07:35.182Z","origin":"live","id":"chatcmpl-tool-a549f5938b4d60ee","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":65},{"path":"PA14 quorum sensing/project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:07:37.204Z","origin":"live","id":"chatcmpl-tool-87ae6a2c21aa0238","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":76},{"path":"PA14 quorum sensing/project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:08:17.319Z","origin":"live","id":"chatcmpl-tool-8cb7dc915ddc4fa2","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":64},{"path":"PA14 quorum sensing/project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:10:19.593Z","origin":"live","id":"chatcmpl-tool-8de2edd619034840","locations":[{"path":"PA14 quorum sensing/project-notes.md","line":64},{"path":"PA14 quorum sensing/project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:10:47.974Z","origin":"live","id":"chatcmpl-tool-beb256a58642eedc","locations":[],"tool":"Bash","outcome":"returned"},{"at":"2026-11-01T17:10:54.634Z","origin":"live","id":"chatcmpl-tool-8c51cf1fcd7e00fc","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"}],"config":{"at":"2026-11-01T16:56:10.108Z","origin":"initial","options":[{"id":"mode","name":"Mode","category":"mode","description":"Session permission mode","type":"select","current":"default","values":[{"value":"default","name":"Manual","description":"Always ask before making changes"},{"value":"acceptEdits","name":"Accept edits","description":"Automatically accept all file edits"},{"value":"plan","name":"Plan","description":"Create a plan before making changes"},{"value":"auto","name":"Auto","description":"Claude handles permission decisions"},{"value":"bypassPermissions","name":"Bypass permissions","description":"Accepts all permissions"}]},{"id":"model","name":"Model","category":"model","description":"AI model to use","type":"select","current":"westlakehpc/deepseek-v4.1-flash[1m]","values":[{"value":"westlakehpc/deepseek-v4.1-flash[1m]","name":"DeepSeek V4.1 Flash"}]},{"id":"effort","name":"Effort","category":"thought_level","description":"Available effort levels for this model","type":"select","current":"xhigh","values":[{"value":"default","name":"Default"},{"value":"low","name":"Low"},{"value":"medium","name":"Medium"},{"value":"high","name":"High"},{"value":"xhigh","name":"Xhigh"},{"value":"max","name":"Max"}]},{"id":"ultracode","name":"Ultracode","category":"model_config","description":"Dynamic workflows on every task, at any effort level","type":"select","current":"off","values":[{"value":"on","name":"On"},{"value":"off","name":"Off"}]}],"omitted":0}}}
+{"format":2,"backend":"claude-acp","id":"c-67f77cfebaba2cea","changeId":"q-coculture","requestDigest":"61d3c561c68d630b73ad5f0f06b10b60224ee6787f36f52b516d85f3e194b16f","createdAt":"2026-11-01T16:56:09.463Z","createdBy":"browser:local","updatedAt":"2026-11-01T17:15:39.967Z","version":1894,"client":"claude-code","nativeSessionId":null,"confirmed":true,"principal":"agent:0feaa53ea2a60d61f484b80113fd6373","title":"Now the co-culture experiment: when ΔrhlI and ΔlasI are grown together, do they…","turns":[{"id":"t1","changeId":"q-coculture","requestDigest":"61d3c561c68d630b73ad5f0f06b10b60224ee6787f36f52b516d85f3e194b16f","by":"browser:local","text":"Now the co-culture experiment: when ΔrhlI and ΔlasI are grown together, do they swarm like wild type again, and does it depend on the ratio they are mixed at? I care about where the peak is and how strong the ratio effect is. Same rules: R, a figure and a table in results/. One clean figure is enough — do not spend several rounds restyling it.","sentAt":"2026-11-01T16:56:09.463Z","state":"completed","startedAt":"2026-11-01T16:56:09.608Z","endedAt":"2026-11-01T17:11:38.991Z","pid":44481,"model":"westlakehpc/deepseek-v4.1-flash[1m]","stop":null,"exit":null,"steps":[{"kind":"tool","at":"2026-11-01T16:56:18.770Z","id":"chatcmpl-tool-83759658882c8160","tool":"Bash","title":"rtk ls PA14 quorum sensing","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:17.174Z","detail":"rtk ls PA14 quorum sensing","purpose":"List project files","output":{"text":"analysis/\ndata/\nresults/\nREADME.md  1.9K\nproject-notes.md  5.8K","lines":5,"bytes":63,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:18.873Z","id":"chatcmpl-tool-b0cc7a797ff3783e","tool":"Bash","title":"cat PA14 quorum sensing/project-notes.md 2>/dev/null | head -100","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:17.494Z","detail":"cat PA14 quorum sensing/project-notes.md 2>/dev/null | head -100","purpose":"Show existing project notes","output":{"text":"- Used circularity as the primary shape readout and roundness as a check on elongation (the usual reading of these imaging-software metrics; the data sheet does not give their formulas). The two disagree in a useful way: circularity changes strongly while roundness does not, which points to the colony perimeter rather than elongation. See [results/swarming_single_mutants_summary.csv](results/swarming_single_mutants_summary.csv).\n- Added a secondary comparison of rhl mutants against las mutants, pooling the two mutants of each system (6 vs 6 dishes). It is exploratory, not a pre-specified contrast; the per-mutant results show the same ordering. See [results/swarming_system_contrast.csv](results/swarming_system_contrast.csv).\n\n### Files\n\n- [analysis/swarming_single_mutants.R](analysis/swarming_single_mutants.R) — the analysis: data reading, Welch comparisons, assumption checks, sensitivity analyses and the figure; writes the three result files.\n- [results/swarming_single_mutants_summary.csv](results/swarming_single_mutants_summary.csv) — one row per genotype: area, circularity and roundness means and SDs, ratios or differences versus wild type with 95% CIs, and Holm-adjusted p-values.\n- [results/swarming_system_contrast.csv](results/swarming_system_contrast.csv) — rhl mutants versus las mutants for area, circularity and roundness.\n- [results/swarming_single_mutants.png](results/swarming_single_mutants.png) — three-panel figure of area, circularity and roundness by genotype.\n\n### To do\n\n- [x] Explore the swarming data and check distributions\n- [x] Write and run the R analysis\n- [x] Write figure and numeric table to results/","lines":47,"bytes":5903,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:23.713Z","id":"chatcmpl-tool-9c6f61581ee3772e","tool":"Bash","title":"rtk ls PA14 quorum sensing/data PA14 quorum sensing/data/swarming PA14 quorum sensing/results PA14 quorum sensing/analysis 2>/dev/null","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:21.630Z","detail":"rtk ls PA14 quorum sensing/data PA14 quorum sensing/data/swarming PA14 quorum sensing/results PA14 quorum sensing/analysis 2>/dev/null","purpose":"List data, results, analysis directories","output":{"text":"rnaseq/\nswarming/\nswarming_cocultures.R  27.2K\nswarming_single_mutants.R  12.4K\ncocultures.csv  1.8K\nsingle_cultures.csv  612B\nswarming_single_mutants.png  164.1K\nswarming_single_mutants_summary.csv  1.2K\nswarming_system_contrast.csv  302B\n... (4 filtered)","lines":10,"bytes":256,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:25.737Z","id":"chatcmpl-tool-84a44fcec3fa3733","tool":"Bash","title":"cat PA14 quorum sensing/README.md","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:21.983Z","detail":"cat PA14 quorum sensing/README.md","purpose":"Read project README","output":{"text":"\n## Data\n\n| File | What it holds |\n| --- | --- |\n| [data/swarming/single_cultures.csv](data/swarming/single_cultures.csv) | Swarming of wild type and the four single mutants, one dish per row: the colony `area` and `circularity` the imaging software reports, three replicates each. |\n| [data/swarming/cocultures.csv](data/swarming/cocultures.csv) | Swarming of wild type, ΔlasI and ΔrhlI grown alone, and of ΔrhlI:ΔlasI mixes at eleven ratios from 1:3 to 1000:1, three replicates each. `ratio_rhlI_to_lasI` reads ΔrhlI first, so 10:1 is ten ΔrhlI cells per ΔlasI cell. |\n| [data/rnaseq/counts.csv](data/rnaseq/counts.csv) | Raw RNA-seq counts, one row per gene and one column per sample. |\n| [data/rnaseq/samples.csv](data/rnaseq/samples.csv) | What each sample column is: `Media` (MMGluFeMinus, MMGluFePlus, Succinate) × `Strain` (1 wild type, 97 ΔrhlI, 98 ΔlasI, 99 ΔlasIΔrhlI) × `Replicate` (A, B, C). |\n| [data/rnaseq/annotation.csv](data/rnaseq/annotation.csv) | Each locus tag's gene name and product. |\n\nThe data come with the study\n([microPublication Biology, 10.17912/micropub.biology.001326](https://doi.org/10.17912/micropub.biology.001326));\nthe counts and sample sheet are as distributed with it, and the annotation keeps the three\ncolumns this project reads.\n\n## Notes\n\n`area` is in the units the imaging software reports, so it is compared within the assay and\nnever across assays. The swarming assay has three replicates per condition.","lines":29,"bytes":1912,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:35.773Z","id":"chatcmpl-tool-99f6faa46fd24ef8","tool":"Bash","title":"ls -la PA14 quorum sensing/results/ PA14 quorum sensing/analysis/ PA14 quorum sensing/data/swarming/","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:35.090Z","detail":"ls -la PA14 quorum sensing/results/ PA14 quorum sensing/analysis/ PA14 quorum sensing/data/swarming/","purpose":"List directories in full without filtering","output":{"text":"644  swarming_cocultures.R  27.2K\n644  swarming_single_mutants.R  12.4K\n644  cocultures.csv  1.8K\n644  single_cultures.csv  612B\n644  swarming_single_mutants.png  164.1K\n644  swarming_single_mutants_summary.csv  1.2K\n644  swarming_system_contrast.csv  302B\n... (3 filtered)","lines":8,"bytes":273,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:35.802Z","id":"chatcmpl-tool-a1081938778e555d","tool":"Bash","title":"cat PA14 quorum sensing/data/swarming/cocultures.csv","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:35.617Z","detail":"cat PA14 quorum sensing/data/swarming/cocultures.csv","purpose":"Read coculture data","output":{"text":"26,ΔrhlI:ΔlasI,4:1,B,130242,0.065,0.974\n27,ΔrhlI:ΔlasI,4:1,C,189336,0.039,0.964\n28,ΔrhlI:ΔlasI,5:1,A,127082,0.058,0.886\n29,ΔrhlI:ΔlasI,5:1,B,122640,0.069,0.847\n30,ΔrhlI:ΔlasI,5:1,C,104537,0.073,0.965\n31,ΔrhlI:ΔlasI,10:1,A,129141,0.055,0.952\n32,ΔrhlI:ΔlasI,10:1,B,185482,0.038,0.908\n33,ΔrhlI:ΔlasI,10:1,C,238479,0.034,0.971\n34,ΔrhlI:ΔlasI,50:1,A,92265,0.093,0.919\n35,ΔrhlI:ΔlasI,50:1,B,116187,0.066,0.976\n36,ΔrhlI:ΔlasI,50:1,C,73305,0.126,0.734\n37,ΔrhlI:ΔlasI,100:1,A,85812,0.095,0.953\n38,ΔrhlI:ΔlasI,100:1,B,85686,0.095,0.943\n39,ΔrhlI:ΔlasI,100:1,C,51863,0.144,0.624\n40,ΔrhlI:ΔlasI,500:1,A,10623,0.747,0.99\n41,ΔrhlI:ΔlasI,500:1,B,9175,0.856,0.972\n42,ΔrhlI:ΔlasI,500:1,C,10341,0.853,0.8\n43,ΔrhlI:ΔlasI,1000:1,A,14736,0.634,0.834\n44,ΔrhlI:ΔlasI,1000:1,B,73579,0.107,0.977\n45,ΔrhlI:ΔlasI,1000:1,C,47991,0.166,0.99","lines":46,"bytes":1878,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:40.280Z","id":"chatcmpl-tool-abc49b91b018a8de","tool":"Bash","title":"find PA14 quorum sensing -maxdepth 2 -type f | sort; echo ---; cd PA14 quorum sensing && git status --short | head -30; echo ---; git log --oneline -5","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:56:40.162Z","detail":"find PA14 quorum sensing -maxdepth 2 -type f | sort; echo ---; cd PA14 quorum sensing && git status --short | head -30; echo ---; git log --oneline -5","purpose":"List all files and git state of example project","output":{"text":" M ../../../src/contract.generated.ts\n M ../../../src/conversations.ts\n M ../../../src/protocol.ts\n M ../../../src/server.ts\n M ../../../src/state.ts\n M ../../../web/conversation.tsx\n?? ../../../final4.mjs\n?? ../../../findover.mjs\n?? ../../../narrow.mjs\n?? ../../../overlap.mjs\n?? ../../../shot-artifact.mjs\n?? ../../../shot2.mjs\n?? ../../../shot3.mjs\n?? ../../../shot3all.mjs\n?? ../../../src/example-project.ts---\n7c19d4a4 Record the 0.5.2 candidate for macOS and Linux\nf95906a3 Say why a Core cannot be used instead of printing a stack\n7f0ddc25 Pack one Core per platform and open folders on Linux desktops\na2b752d8 Record the 0.5.2 candidate packed without Agent clients\ne55a7028 Have the doctor say whether Claude Code and Codex are installed","lines":35,"bytes":1702,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:56:44.577Z","id":"chatcmpl-tool-988897ec9d449ddf","tool":"Read","title":"Read analysis/swarming_cocultures.R","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T16:56:44.547Z","detail":"analysis/swarming_cocultures.R"},{"kind":"text","at":"2026-11-01T16:57:31.713Z","id":"msg_resp_bf5f6a4a96777f5b","text":"I'll set up the session notes first, then examine the data and the existing script.\n\n"},{"kind":"tool","at":"2026-11-01T16:57:39.872Z","id":"chatcmpl-tool-b087af16f229c819","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:57:38.173Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T16:57:43.495Z","id":"chatcmpl-tool-8ee84775ea50fe4e","tool":"ToolSearch","title":"ToolSearch","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:57:43.476Z","detail":"select:mcp__rho__rho_index,mcp__rho__rho_resolve,mcp__rho__rho_call,mcp__rho__rho_read"},{"kind":"tool","at":"2026-11-01T16:57:46.402Z","id":"chatcmpl-tool-9758dd4b962f092f","tool":"Bash","title":"Rscript -e 'cat(R.version.string, \"\\n\"); for (p in c(\"dplyr\",\"ggplot2\",\"patchwork\",\"car\")) cat(p, requireNamespace(p, quietly=TRUE), \"\\n\")'","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:57:44.342Z","detail":"Rscript -e 'cat(R.version.string, \"\\n\"); for (p in c(\"dplyr\",\"ggplot2\",\"patchwork\",\"car\")) cat(p, requireNamespace(p, quietly=TRUE), \"\\n\")'","purpose":"Check R version and required packages","output":{"text":"R version 4.5.2 (2025-10-31) \ndplyr TRUE \nggplot2 TRUE \npatchwork TRUE \ncar TRUE","lines":5,"bytes":80,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:57:49.245Z","id":"chatcmpl-tool-8aa652add5b9b56a","tool":"mcp__rho__rho_index","title":"mcp__rho__rho_index","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:57:49.134Z"},{"kind":"tool","at":"2026-11-01T16:57:51.909Z","id":"chatcmpl-tool-b5d7e844d6f9a09c","tool":"Bash","title":"stat -f '%Sm %N' -t '%Y-%m-%d %H:%M' analysis/*.R data/swarming/*.csv results/* project-notes.md","toolKind":"execute","outcome":"rejected","startedAt":"2026-11-01T16:57:50.103Z","detail":"stat -f '%Sm %N' -t '%Y-%m-%d %H:%M' analysis/*.R data/swarming/*.csv results/* project-notes.md","purpose":"Show file modification times","output":{"text":"User refused permission to run tool","lines":1,"bytes":35,"cut":false}},{"kind":"tool","at":"2026-11-01T16:57:54.567Z","id":"chatcmpl-tool-8924b8566aacf77c","tool":"mcp__rho__rho_resolve","title":"mcp__rho__rho_resolve","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:57:53.487Z"},{"kind":"tool","at":"2026-11-01T16:58:06.797Z","id":"chatcmpl-tool-a53c6af8b86531c1","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:04.094Z","operation":"kernel.read"},{"kind":"tool","at":"2026-11-01T16:58:08.750Z","id":"chatcmpl-tool-b6668bdd2a225622","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T16:58:08.690Z","detail":"/sessions"},{"kind":"tool","at":"2026-11-01T16:58:11.740Z","id":"chatcmpl-tool-87aa2178f2f0ce21","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T16:58:11.695Z","detail":"sessions"},{"kind":"tool","at":"2026-11-01T16:58:13.710Z","id":"chatcmpl-tool-b6a231969dc8b6fc","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:13.132Z"},{"kind":"tool","at":"2026-11-01T16:58:15.330Z","id":"chatcmpl-tool-8da822b37ed8843b","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:15.273Z","detail":"/value"},{"kind":"tool","at":"2026-11-01T16:58:21.337Z","id":"chatcmpl-tool-94bc1dff3abc63d1","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:21.282Z","detail":"/value/sessions"},{"kind":"tool","at":"2026-11-01T16:58:26.867Z","id":"chatcmpl-tool-b6f13be6e2f6e28e","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:26.810Z","detail":"/value/cells"},{"kind":"tool","at":"2026-11-01T16:58:29.670Z","id":"chatcmpl-tool-82c643d5496a891a","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:29.608Z","detail":"/value/cells/17"},{"kind":"tool","at":"2026-11-01T16:58:42.837Z","id":"chatcmpl-tool-97fae9de5ea8a4b6","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:42.784Z","detail":"/value/cells/16"},{"kind":"tool","at":"2026-11-01T16:58:42.949Z","id":"chatcmpl-tool-bdffc473b5a743fe","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:42.898Z","detail":"/value/cells/15"},{"kind":"tool","at":"2026-11-01T16:58:49.047Z","id":"chatcmpl-tool-b6df29e2160fba39","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:48.992Z","detail":"/value/cells/14"},{"kind":"tool","at":"2026-11-01T16:58:49.582Z","id":"chatcmpl-tool-a6a7eb5eb8fa3150","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:49.528Z","detail":"/value/cells/13"},{"kind":"tool","at":"2026-11-01T16:58:52.285Z","id":"chatcmpl-tool-beeca28f286edc05","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:52.235Z","detail":"/value/cells/14/outputs"},{"kind":"tool","at":"2026-11-01T16:58:53.691Z","id":"chatcmpl-tool-9a7f20d639074cfb","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:53.631Z","detail":"/value/cells/13/outputs"},{"kind":"tool","at":"2026-11-01T16:58:55.258Z","id":"chatcmpl-tool-84eb28f9f2610671","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:55.206Z","detail":"/value/cells/14/outputs/0/text"},{"kind":"tool","at":"2026-11-01T16:58:58.184Z","id":"chatcmpl-tool-a24d1f1b0e63b5f0","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:58:58.128Z","detail":"/value/cells/13/outputs/0/text"},{"kind":"text","at":"2026-11-01T17:00:22.995Z","id":"msg_resp_964131adcceda004","text":"The co-culture script was prepared in an earlier, now-ended R session but no results were written. I'll validate its key numbers independently in a fresh live R session, then run it.\n\n"},{"kind":"tool","at":"2026-11-01T17:00:32.445Z","id":"chatcmpl-tool-8dd6945784d8a5e5","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T17:00:23.154Z"},{"kind":"tool","at":"2026-11-01T17:00:44.976Z","id":"chatcmpl-tool-9bffba28deeac9f8","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:00:43.645Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:01:07.429Z","id":"chatcmpl-tool-92c90b4ce3d359a6","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:01:02.388Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:01:31.512Z","id":"chatcmpl-tool-8d498cdb0c2fbca7","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:01:13.614Z","operation":"kernel.run"},{"kind":"text","at":"2026-11-01T17:02:15.931Z","id":"msg_resp_b0a84a4ae7152853","text":"Independent checks reproduce the prepared model: peak 12.3:1 (bootstrap 95% CI 10.4–14.7), quadratic R² 0.89, one-way ratio R² 0.93. Now I'll run the full script to write the result files and figure.\n\n"},{"kind":"tool","at":"2026-11-01T17:02:19.472Z","id":"chatcmpl-tool-83e899c6387d50f5","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:02:15.932Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:02:33.917Z","id":"chatcmpl-tool-80d6d7cb2533b591","tool":"Read","title":"Read results/swarming_cocultures_summary.csv","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:02:33.896Z","detail":"results/swarming_cocultures_summary.csv"},{"kind":"tool","at":"2026-11-01T17:02:34.332Z","id":"chatcmpl-tool-b0f6d7b0f487660b","tool":"Read","title":"Read results/swarming_cocultures_ratio_model.csv","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:02:34.314Z","detail":"results/swarming_cocultures_ratio_model.csv"},{"kind":"tool","at":"2026-11-01T17:02:36.333Z","id":"chatcmpl-tool-8f2ec59002d4b779","tool":"Read","title":"Read results/swarming_cocultures.png","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:02:36.180Z","detail":"results/swarming_cocultures.png"},{"kind":"text","at":"2026-11-01T17:04:15.829Z","id":"msg_resp_9c4f255399978a20","text":"The script wrote all three result files. Before writing the findings, I'll check one interpretive point: whether the fitted peak is distinguishable from wild type once wild-type dish variability is included, and the overall ratio ANOVA.\n\n\n\n"},{"kind":"tool","at":"2026-11-01T17:04:21.776Z","id":"chatcmpl-tool-a7717366a2c3d402","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:04:15.829Z","operation":"kernel.run"},{"kind":"text","at":"2026-11-01T17:04:58.630Z","id":"msg_resp_aa538e63bf0d58d0","text":"The peak-to-wild-type bootstrap (resampling both mix and wild-type dishes) gives 0.99–1.70, so the peak is statistically indistinguishable from wild type. That belongs in the result table, so I'll add it and the one-way ratio p-value to the script, then re-run.\n\n"},{"kind":"tool","at":"2026-11-01T17:05:06.774Z","id":"chatcmpl-tool-b67503b704a95a97","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:04.844Z","detail":"analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:12.806Z","id":"chatcmpl-tool-a1e0e2d1aa7e465f","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:11.743Z","detail":"analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:18.841Z","id":"chatcmpl-tool-ae8cdd54746f8082","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:16.847Z","detail":"analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:24.863Z","id":"chatcmpl-tool-a6d1b3c2dfab27cd","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:23.179Z","detail":"analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:30.901Z","id":"chatcmpl-tool-b25c09ec1e9ffc25","tool":"Edit","title":"Edit analysis/swarming_cocultures.R","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:05:30.036Z","detail":"analysis/swarming_cocultures.R"},{"kind":"tool","at":"2026-11-01T17:05:38.426Z","id":"chatcmpl-tool-b8151231bba7b10e","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:05:33.364Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T17:05:43.005Z","id":"chatcmpl-tool-8d7ce51e52a0c488","tool":"Bash","title":"grep -n 'peak_over_wildtype\\|ratio_one_way_p\\|one_way_p' results/swarming_cocultures_ratio_model.csv; echo ---; ls -l results/","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T17:05:41.979Z","detail":"grep -n 'peak_over_wildtype\\|ratio_one_way_p\\|one_way_p' results/swarming_cocultures_ratio_model.csv; echo ---; ls -l results/","purpose":"Check new model rows and result files","output":{"text":"9:\"area\",\"ratio_one_way_p\",1.23629e-09,NA,NA,\"one-way ANOVA F test across the 10 window ratios\"\n12:\"area\",\"peak_over_wildtype\",1.34221,0.989285,1.71213,\"fitted peak geometric mean / wild-type geometric mean; bootstrap 95% CI resampling mix and wild-type dishes\"\n---\n644  swarming_cocultures.png  228.6K\n644  swarming_cocultures_ratio_model.csv  4.2K\n644  swarming_cocultures_summary.csv  3.3K\n644  swarming_single_mutants.png  164.1K\n644  swarming_single_mutants_summary.csv  1.2K\n644  swarming_system_contrast.csv  302B","lines":9,"bytes":520,"cut":false},"exitCode":0},{"kind":"text","at":"2026-11-01T17:06:31.254Z","id":"msg_resp_a338e57a36af850f","text":"All result files are in place. Now I'll write the findings into the session notes.\n\n"},{"kind":"tool","at":"2026-11-01T17:06:33.198Z","id":"chatcmpl-tool-a31f6867366b5a60","tool":"Read","title":"Read project-notes.md (from line 55)","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:06:33.178Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:09.093Z","id":"chatcmpl-tool-afa93163df2807bd","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:07.826Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:13.784Z","id":"chatcmpl-tool-91469059f68c4d4a","tool":"Read","title":"Read project-notes.md (from line 48)","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T17:07:13.765Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:33.151Z","id":"chatcmpl-tool-98f42ffae1befa60","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:31.670Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:35.182Z","id":"chatcmpl-tool-a549f5938b4d60ee","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:33.141Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:07:37.204Z","id":"chatcmpl-tool-87ae6a2c21aa0238","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:07:34.781Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:08:17.319Z","id":"chatcmpl-tool-8cb7dc915ddc4fa2","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:08:15.832Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T17:10:19.593Z","id":"chatcmpl-tool-8de2edd619034840","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T17:10:18.645Z","detail":"project-notes.md"},{"kind":"text","at":"2026-11-01T17:10:41.443Z","id":"msg_resp_ba1d3c9f48ea6588","text":"The notes are updated. One last check: run the saved script standalone with `Rscript` to confirm the results reproduce without the live session.\n\n"},{"kind":"tool","at":"2026-11-01T17:10:47.974Z","id":"chatcmpl-tool-beb256a58642eedc","tool":"Bash","title":"Rscript analysis/swarming_cocultures.R 2>&1 | tail -25","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T17:10:42.754Z","detail":"Rscript analysis/swarming_cocultures.R 2>&1 | tail -25","purpose":"Run the co-culture analysis script standalone","output":{"text":"Multiple R-squared:  0.8908,\tAdjusted R-squared:  0.8827 \nF-statistic: 110.2 on 2 and 27 DF,  p-value: 1.034e-13\n\nPeak ratio: 12.27 :1  95% CI 10.4-14.67 \nPeak area: 145880  95% CI 132127-161011 \nPeak / wild type: 1.34  95% CI 0.99-1.71 \nWild-type geometric mean: 108686 \nFitted area reaches the wild-type mean between ratios 3.24 and 46.4 \nOne-way ratio R2: 0.93  quadratic R2: 0.891 \nSensitivity peaks: all 12 = 15.63 ; excl 1000:1 = 11.16 ; excl 500:1 = 22.36 \nLeave-one-ratio-out peaks: 12.32 12.28 11.89 12.2 11.9 12.81 12.12 12.41 13.05 11.62 \n\nCircularity minimum at 12.22 :1; fitted 0.05 vs wild type 0.061 \nRoundness fitted maximum at 12.17 :1; fitted 0.97 vs wild type 0.855 \n\nAssumption checks: Levene p = 0.939 ; Shapiro p = 0.666 ; max Cook's D = 0.184 \n\nWrote results/swarming_cocultures_summary.csv\nWrote results/swarming_cocultures_ratio_model.csv\nWrote results/swarming_cocultures.png","lines":25,"bytes":1100,"cut":true},"exitCode":0},{"kind":"tool","at":"2026-11-01T17:10:54.635Z","id":"chatcmpl-tool-8c51cf1fcd7e00fc","tool":"mcp__rho__rho_read","title":"mcp__rho__rho_read","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T17:10:54.077Z"},{"kind":"text","at":"2026-11-01T17:11:38.970Z","id":"msg_resp_9af7b0624738af67","text":"Yes — co-culture restores swarming, and the ratio matters strongly.\n\n**Peak.** The fitted optimum is **12.3:1 ΔrhlI:ΔlasI** (cluster-bootstrap 95% CI **10.4–14.7:1**). At the peak, fitted area is **145,880** versus a wild-type geometric mean of **108,686** — **1.34× wild type** (95% CI **0.99–1.71**). The nearest observed mix, 10:1, was 1.64× wild type (0.83–3.25, unadjusted p = 0.11), so the peak is statistically indistinguishable from wild type, not significantly above it. For comparison, ΔrhlI alone was 0.094× and ΔlasI alone 0.134× wild type, so the peak is about 14× and 10× their own areas.\n\n**Ratio effect.** Across the ten well-sampled ratios (1:3–100:1), the mixing ratio explains **93% of the variance in log area** (one-way ANOVA F(9,20) = 29.5, p = 1.2 × 10⁻⁹; quadratic R² = 0.891 versus 0.364 for a linear fit). The fitted peak is **8.7×** the 1:3 value, **2.1×** the 100:1 value and **14.5×** the 500:1 value. Fitted area reaches wild-type level between **3.2:1 and 46.4:1**. Beyond that, rescue collapses at 500:1 (0.09× wild type, the only mix significantly below wild type after Holm, p = 0.037) and is heterogeneous at 1000:1 (0.34×, CI 0.06–2.14). Shape converges on the same optimum: circularity reaches its minimum at 12.2:1 and roundness its maximum at 12.2:1.\n\n**Caveats.** Three dishes per condition; the low-ratio pairwise reductions (0.17–0.39× wild type) are only borderline after Holm correction (p = 0.073–0.121), so the overall model carries that part of the conclusion. The peak location depends on the fitted window: including all twelve ratios gives 15.6:1 but a poor fit (R² 0.66), while excluding only 500:1 or only 1000:1 gives 22.4:1 or 11.2:1. Within the observed rescue window, leave-one-ratio-out peaks span 11.6–13.1.\n\nFiles:\n- [analysis/swarming_cocultures.R](analysis/swarming_cocultures.R) — full analysis, reproduces everything with `Rscript analysis/swarming_cocultures.R`\n- [results/swarming_cocultures_summary.csv](results/swarming_cocultures_summary.csv) — per-condition table with comparisons versus wild type\n- [results/swarming_cocultures_ratio_model.csv](results/swarming_cocultures_ratio_model.csv) — peak, ratio effect, sensitivity and diagnostic table\n- [results/swarming_cocultures.png](results/swarming_cocultures.png) — one three-panel figure (area, circularity, roundness)\n\nThe shared notes are updated in [project-notes.md](project-notes.md)."}],"omitted":0,"retry":null,"result":{"isError":false,"kind":"acp","reason":"end_turn","steps":null,"durationMs":929384,"costUsd":null,"message":null},"problem":null,"evidence":{"records":[{"key":"command:chatcmpl-tool-b0cc7a797ff3783e:undefined:project-notes.md","path":"project-notes.md","phase":"command:chatcmpl-tool-b0cc7a797ff3783e:undefined","requestedAt":"2026-11-01T16:56:17.386Z","state":"captured","snapshots":[{"resource":{"id":"9678539599c516fbc3e2d54614d7f89b299ca0edf9fae04c8eb053c7cdac21c2","version":"03bd35607b650b6c13336489c010d620a4e1a7e7204042cbf10fa47ac77af97a"},"kind":"file","bytes":5904,"observedAt":"2026-11-01T16:56:17.421Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"command:chatcmpl-tool-84a44fcec3fa3733:undefined:README.md","path":"README.md","phase":"command:chatcmpl-tool-84a44fcec3fa3733:undefined","requestedAt":"2026-11-01T16:56:21.798Z","state":"captured","snapshots":[{"resource":{"id":"8335a7f50594c96793bc5243e62e561d84b542c23802378deb7c8907fc467447","version":"56924e744562b67c05bb53bad2914c31ed4997eb1e7c7ef6e58e37080e049d09"},"kind":"file","bytes":1913,"observedAt":"2026-11-01T16:56:21.837Z","source":{"kind":"disk","path":"README.md"}}]},{"key":"command:chatcmpl-tool-a1081938778e555d:undefined:data/swarming/cocultures.csv","path":"data/swarming/cocultures.csv","phase":"command:chatcmpl-tool-a1081938778e555d:undefined","requestedAt":"2026-11-01T16:56:35.360Z","state":"captured","snapshots":[{"resource":{"id":"2877ce204ee89e35151335d1be02c23e13b79868f8fb9d12969178265b6450eb","version":"b1b12af73ab2e4ce4a19a2295a85cb485241c1223dd71ef54313a0c206c87a33"},"kind":"table","bytes":1879,"observedAt":"2026-11-01T16:56:35.407Z","source":{"kind":"disk","path":"data/swarming/cocultures.csv"}}]},{"key":"tool:chatcmpl-tool-988897ec9d449ddf:requested:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-988897ec9d449ddf:requested","requestedAt":"2026-11-01T16:56:44.547Z","state":"captured","snapshots":[{"resource":{"id":"1f1eb2c001a34e511db6575708978dfd54e8fbe20fd21dfc5742da12781da6cf","version":"7c473232d1a129f4ebb7704a20a67aa6088eb55c1ad1d0dd90f37c36251630f1"},"kind":"file","bytes":27885,"observedAt":"2026-11-01T16:56:44.582Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-b087af16f229c819:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-b087af16f229c819:returned","requestedAt":"2026-11-01T16:57:39.872Z","state":"captured","snapshots":[{"resource":{"id":"66512b5f72c9ac74714c2c3b55975d8eab987d49d216739e2c2d53be7ab707be","version":"bca642094971b5fe7769377a249d2587e79980c8043cdcc9d9f19e3403d8ad23"},"kind":"file","bytes":7306,"observedAt":"2026-11-01T16:57:39.926Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-80d6d7cb2533b591:requested:results/swarming_cocultures_summary.csv","path":"results/swarming_cocultures_summary.csv","phase":"tool:chatcmpl-tool-80d6d7cb2533b591:requested","requestedAt":"2026-11-01T17:02:33.896Z","state":"captured","snapshots":[{"resource":{"id":"dbec0f2c3a8daf9012a5ca95678df3e70b06bcd37edf5ab79c6b265301b2e91b","version":"2519bcb743fdede4abbe09cefa70a761d3276ea00ecfb200a3f2a7c7a1580381"},"kind":"table","bytes":3407,"observedAt":"2026-11-01T17:02:33.933Z","source":{"kind":"disk","path":"results/swarming_cocultures_summary.csv"}}]},{"key":"tool:chatcmpl-tool-b0f6d7b0f487660b:requested:results/swarming_cocultures_ratio_model.csv","path":"results/swarming_cocultures_ratio_model.csv","phase":"tool:chatcmpl-tool-b0f6d7b0f487660b:requested","requestedAt":"2026-11-01T17:02:34.314Z","state":"captured","snapshots":[{"resource":{"id":"d9cd275ad886225d1f115731a20522998ab16f59c44b1d519cfa42cb764570b7","version":"9b46e669452e972f12f49ab47f64daa571d8d1a3b80a591f9028105feb2a8d10"},"kind":"table","bytes":4157,"observedAt":"2026-11-01T17:02:34.350Z","source":{"kind":"disk","path":"results/swarming_cocultures_ratio_model.csv"}}]},{"key":"tool:chatcmpl-tool-8f2ec59002d4b779:requested:results/swarming_cocultures.png","path":"results/swarming_cocultures.png","phase":"tool:chatcmpl-tool-8f2ec59002d4b779:requested","requestedAt":"2026-11-01T17:02:36.180Z","state":"captured","snapshots":[{"resource":{"id":"cc393e70db0c4ff8d76b62db44f8de288d42af35fa2d537dabf0c49557c1c6a8","version":"94aafdb53e5916fb35ca0eaf7c403ff822c907bf43fed39188772e103cf9c8c6"},"kind":"media","bytes":234096,"observedAt":"2026-11-01T17:02:36.221Z","source":{"kind":"disk","path":"results/swarming_cocultures.png"}}]},{"key":"tool:chatcmpl-tool-b67503b704a95a97:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-b67503b704a95a97:returned","requestedAt":"2026-11-01T17:05:06.774Z","state":"captured","snapshots":[{"resource":{"id":"880bbf79eb2efd54457926608541939342bd6d6457b8dff56e36a64f9d700202","version":"a0641d022a11af6400a9f19a963eccb2ae464fce6c23752360807181ae667df5"},"kind":"file","bytes":28495,"observedAt":"2026-11-01T17:05:06.833Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-a1e0e2d1aa7e465f:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-a1e0e2d1aa7e465f:returned","requestedAt":"2026-11-01T17:05:12.806Z","state":"captured","snapshots":[{"resource":{"id":"e24daf11fe7991c0bb5518b72a217661b2f24b2fe593aeaed0949d5b37cc4717","version":"633d6a61c2263a8be8d5b39b0763613778c20bf41851b5cb37c0e0e57468da2d"},"kind":"file","bytes":28626,"observedAt":"2026-11-01T17:05:12.868Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-ae8cdd54746f8082:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-ae8cdd54746f8082:returned","requestedAt":"2026-11-01T17:05:18.841Z","state":"captured","snapshots":[{"resource":{"id":"4ce0a7aac07e36c2dda77f16fee4ca0db2f66ea0823b8ac1d892f2b30ff43b73","version":"6d0d380b56cccc5f0dbb7e5e6a051b9b9c898b28f055a9e4df130b1f2fa7bcca"},"kind":"file","bytes":28758,"observedAt":"2026-11-01T17:05:18.904Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-a6d1b3c2dfab27cd:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-a6d1b3c2dfab27cd:returned","requestedAt":"2026-11-01T17:05:24.863Z","state":"captured","snapshots":[{"resource":{"id":"4a2f3f58108ffb842da662a571675120e444a7897f2b064df478ae53e56293bf","version":"d5955e8b61fa45349533a9ad2432ee7da065ea20702781d83decdfd4eea68577"},"kind":"file","bytes":28849,"observedAt":"2026-11-01T17:05:24.923Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"tool:chatcmpl-tool-b25c09ec1e9ffc25:returned:analysis/swarming_cocultures.R","path":"analysis/swarming_cocultures.R","phase":"tool:chatcmpl-tool-b25c09ec1e9ffc25:returned","requestedAt":"2026-11-01T17:05:30.901Z","state":"captured","snapshots":[{"resource":{"id":"c1d7ec4d732037c1aec395abc8a8d6b2845acdcd8f91954936e0245cf7181137","version":"553390f7520a6266c4f2b72a4df9e450b5383ddb4ab1ed4f9a17076e7b43bde7"},"kind":"file","bytes":28974,"observedAt":"2026-11-01T17:05:30.962Z","source":{"kind":"disk","path":"analysis/swarming_cocultures.R"}}]},{"key":"command:chatcmpl-tool-8d7ce51e52a0c488:undefined:results/swarming_cocultures_ratio_model.csv","path":"results/swarming_cocultures_ratio_model.csv","phase":"command:chatcmpl-tool-8d7ce51e52a0c488:undefined","requestedAt":"2026-11-01T17:05:41.471Z","state":"captured","snapshots":[{"resource":{"id":"51ac10dda0efe4248cec3eadb2292ca6ffaebe1a3ba7e11352a18ddcb94aa26b","version":"6ea552f15c636fe63addf0ca67c93a4a8cc866a7699e925ca9fe112f5b7a4123"},"kind":"table","bytes":4316,"observedAt":"2026-11-01T17:05:41.529Z","source":{"kind":"disk","path":"results/swarming_cocultures_ratio_model.csv"}}]},{"key":"tool:chatcmpl-tool-afa93163df2807bd:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-afa93163df2807bd:returned","requestedAt":"2026-11-01T17:07:09.093Z","state":"captured","snapshots":[{"resource":{"id":"fdc072913da27e66864b86609b041dec9f83c2ab5b3a045c5c9961f51b75cd49","version":"36ce157e29eb6299bf44523078bdc3e3c9422fc541a31b030609fc3571d593d4"},"kind":"file","bytes":13145,"observedAt":"2026-11-01T17:07:09.151Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-98f42ffae1befa60:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-98f42ffae1befa60:returned","requestedAt":"2026-11-01T17:07:33.151Z","state":"captured","snapshots":[{"resource":{"id":"5bcbcb5366e1246d6546d77758c8bbeefc92354129bb3f62d56638bb55f31c50","version":"3f0337a2e0b2bca1b2c1f97b5d5a385f3e6f3997cb6ec135e3338ceb41a86a11"},"kind":"file","bytes":13155,"observedAt":"2026-11-01T17:07:33.209Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-a549f5938b4d60ee:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-a549f5938b4d60ee:returned","requestedAt":"2026-11-01T17:07:35.182Z","state":"captured","snapshots":[{"resource":{"id":"ac7c3acef2c511ab3276071f1d4f8c78633755a57254471c7266cbe361437411","version":"8fad929a7edd138583741fadec37e1bdc995ee7644416dabc7c0d8573d2c5f50"},"kind":"file","bytes":13295,"observedAt":"2026-11-01T17:07:35.239Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-87ae6a2c21aa0238:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-87ae6a2c21aa0238:returned","requestedAt":"2026-11-01T17:07:37.204Z","state":"captured","snapshots":[{"resource":{"id":"de430b43443f9cde4a9a69a3467f662eaf3c264e1a788ea61212de27e5909cd3","version":"22ff16a058c9fd5a787d8376812fba2ca0a160717649bf2a38165ab0f044a307"},"kind":"file","bytes":13307,"observedAt":"2026-11-01T17:07:37.264Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-8cb7dc915ddc4fa2:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-8cb7dc915ddc4fa2:returned","requestedAt":"2026-11-01T17:08:17.319Z","state":"captured","snapshots":[{"resource":{"id":"fbfba969896f136f9e82eccd97ebdbef67a399243fe4d49c217719fb98108aef","version":"c2d5bb55680c49cb7c6f438bc5e7f32ab4989861632558dfde516a2bdce4148b"},"kind":"file","bytes":13402,"observedAt":"2026-11-01T17:08:17.378Z","source":{"kind":"disk","path":"project-notes.md"}}]},{"key":"tool:chatcmpl-tool-8de2edd619034840:returned:project-notes.md","path":"project-notes.md","phase":"tool:chatcmpl-tool-8de2edd619034840:returned","requestedAt":"2026-11-01T17:10:19.593Z","state":"captured","snapshots":[{"resource":{"id":"690166e11c1aa3994bc335f77a69278dbf7360b501ec69334de3998f50df6b91","version":"00c5e3db1d1cc3fa0bf4e4951d7df99f17cd4d2d950feb1ba96080a1f726ebb2"},"kind":"file","bytes":13424,"observedAt":"2026-11-01T17:10:19.653Z","source":{"kind":"disk","path":"project-notes.md"}}]}],"omitted":0,"bytes":514293,"snapshots":20},"permissions":[{"id":"aa6968bd-8c81-4c0c-902c-a30220ccf28e","toolCallId":"chatcmpl-tool-83759658882c8160","title":"rtk ls PA14 quorum sensing","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"90fcef40-17b5-4738-a12c-4b08687e6841","toolCallId":"chatcmpl-tool-9c6f61581ee3772e","title":"rtk ls PA14 quorum sensing/data PA14 quorum sensing/data/swarming PA14 quorum sensing/results PA14 quorum sensing/analysis 2>/dev/null","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"f31a0786-283a-4833-aad4-4cde72c9d49e","toolCallId":"chatcmpl-tool-84a44fcec3fa3733","title":"rtk read PA14 quorum sensing/README.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk read * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"ae84eda5-e523-483c-9558-a057b4235733","toolCallId":"chatcmpl-tool-99f6faa46fd24ef8","title":"rtk ls -la PA14 quorum sensing/results/ PA14 quorum sensing/analysis/ PA14 quorum sensing/data/swarming/","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"be0299de-e2f0-4d4a-83b4-9d821fe37ac6","toolCallId":"chatcmpl-tool-a1081938778e555d","title":"rtk read PA14 quorum sensing/data/swarming/cocultures.csv","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk read * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"24aaaf41-798f-4169-9165-f1589435476b","toolCallId":"chatcmpl-tool-b087af16f229c819","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"dae866e8-3f89-4d1c-80df-f51f7f436068","toolCallId":"chatcmpl-tool-9758dd4b962f092f","title":"Rscript -e 'cat(R.version.string, \"\\n\"); for (p in c(\"dplyr\",\"ggplot2\",\"patchwork\",\"car\")) cat(p, requireNamespace(p, quietly=TRUE), \"\\n\")'","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for similar commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"e0ff4efd-9ea4-4141-8a50-a08ed357caa7","toolCallId":"chatcmpl-tool-b5d7e844d6f9a09c","title":"rtk stat -f '%Sm %N' -t '%Y-%m-%d %H:%M' analysis/*.R data/swarming/*.csv results/* project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk stat * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"reject"},{"id":"355b5915-4edb-4790-8536-70764f3bab60","toolCallId":"chatcmpl-tool-b67503b704a95a97","title":"Edit analysis/swarming_cocultures.R","details":"analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"5f055788-9ea1-4451-8f80-204a47757afe","toolCallId":"chatcmpl-tool-a1e0e2d1aa7e465f","title":"Edit analysis/swarming_cocultures.R","details":"analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"ea7fb496-310b-4da6-bcbd-73c76ca1003c","toolCallId":"chatcmpl-tool-ae8cdd54746f8082","title":"Edit analysis/swarming_cocultures.R","details":"analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"422738dc-8dfb-48a2-bb67-938bf3625411","toolCallId":"chatcmpl-tool-a6d1b3c2dfab27cd","title":"Edit analysis/swarming_cocultures.R","details":"analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"edecd14a-de2d-4345-9cbc-3d908ecc4f82","toolCallId":"chatcmpl-tool-b25c09ec1e9ffc25","title":"Edit analysis/swarming_cocultures.R","details":"analysis/swarming_cocultures.R","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"195ad4a2-399a-4641-8918-9e813a7f823a","toolCallId":"chatcmpl-tool-8d7ce51e52a0c488","title":"rtk grep -n 'peak_over_wildtype\\|ratio_one_way_p\\|one_way_p' results/swarming_cocultures_ratio_model.csv; echo ---; rtk ls -l results/","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for rtk grep * and rtk ls * commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"df8d54e0-f89a-4365-a612-43e8994f8a91","toolCallId":"chatcmpl-tool-afa93163df2807bd","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"34b82c68-1a55-49aa-abd2-44bde9e880f4","toolCallId":"chatcmpl-tool-98f42ffae1befa60","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"b65597d3-cdb2-433a-a4a8-160a1c44215f","toolCallId":"chatcmpl-tool-a549f5938b4d60ee","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"6237174f-5679-4e17-b0b7-06c1f0d61cf3","toolCallId":"chatcmpl-tool-87ae6a2c21aa0238","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"5259caf8-47d4-418f-810d-3825868d0428","toolCallId":"chatcmpl-tool-8cb7dc915ddc4fa2","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"4f2e957c-9639-4868-8e83-2e7a10450f53","toolCallId":"chatcmpl-tool-8de2edd619034840","title":"Edit project-notes.md","details":"project-notes.md","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, allow all edits during this session","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"},{"id":"a7418516-ca89-4a01-8732-077f8b06a08c","toolCallId":"chatcmpl-tool-beb256a58642eedc","title":"Rscript analysis/swarming_cocultures.R 2>&1 | tail -25","options":[{"id":"allow-once","name":"Yes","kind":"allow_once"},{"id":"allow-with-updates","name":"Yes, and don't ask again for Rscript analysis/swarming_cocultures.R commands","kind":"allow_always"},{"id":"reject","name":"No","kind":"reject_once"}],"state":"selected","selected":"allow-once"}],"descriptions":[{"path":"results/swarming_cocultures_summary.csv","version":"2519bcb743fdede4abbe09cefa70a761d3276ea00ecfb200a3f2a7c7a1580381","bytes":3407,"modifiedAt":"2026-11-01T17:10:44.180Z","observedAt":"2026-11-01T17:02:19.667Z","facts":"15 rows × 25 columns: condition, culture, ratio_rhlI_to_lasI, ratio_numeric, n, area_mean, area_sd, area_geomean, … (17 more)","sentence":{"text":"The summary CSV holds 15 co-culture rows and 25 columns, covering wild type, single mutants, and ΔrhlI:ΔlasI mixes from 1:3 to 1000:1, with area, circularity, and roundness statistics.","version":"2519bcb743fdede4abbe09cefa70a761d3276ea00ecfb200a3f2a7c7a1580381","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:02:25.376Z","facts":"15 rows × 25 columns: condition, culture, ratio_rhlI_to_lasI, ratio_numeric, n, area_mean, area_sd, area_geomean, … (17 more)","strategy":"text","cost":{"usd":0.0007769341439999999,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"},{"path":"results/swarming_cocultures_ratio_model.csv","version":"6ea552f15c636fe63addf0ca67c93a4a8cc866a7699e925ca9fe112f5b7a4123","bytes":4316,"modifiedAt":"2026-11-01T17:10:47.403Z","observedAt":"2026-11-01T17:05:44.704Z","facts":"50 rows × 6 columns: metric, quantity, estimate, ci_low, ci_high, detail","sentence":{"text":"This CSV holds 50 rows of co-culture ratio-model results, with columns metric, quantity, estimate, confidence bounds and detail, covering area and circularity fits.","version":"6ea552f15c636fe63addf0ca67c93a4a8cc866a7699e925ca9fe112f5b7a4123","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:05:48.580Z","facts":"50 rows × 6 columns: metric, quantity, estimate, ci_low, ci_high, detail","strategy":"text","cost":{"usd":0.000576200832,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"},{"path":"results/swarming_cocultures.png","version":"94aafdb53e5916fb35ca0eaf7c403ff822c907bf43fed39188772e103cf9c8c6","bytes":234096,"modifiedAt":"2026-11-01T17:10:47.942Z","observedAt":"2026-11-01T17:02:24.666Z","facts":"PNG image, 2760 × 1380 px, 228.6 KB","sentence":{"text":"Three scatter panels plot colony area (log scale), circularity and roundness against ΔrhlI:ΔlasI mix ratio, comparing mix points and fitted curves to Wild type, ΔlasI alone and ΔrhlI alone lines.","version":"94aafdb53e5916fb35ca0eaf7c403ff822c907bf43fed39188772e103cf9c8c6","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:02:37.561Z","facts":"PNG image, 2760 × 1380 px, 228.6 KB","strategy":"image","cost":{"usd":0.000921571776,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"},{"path":"analysis/swarming_cocultures.R","version":"553390f7520a6266c4f2b72a4df9e450b5383ddb4ab1ed4f9a17076e7b43bde7","bytes":28974,"modifiedAt":"2026-11-01T17:05:30.881Z","observedAt":"2026-11-01T17:05:34.702Z","facts":"R script, 669 lines, 11 functions","sentence":{"text":"An R script analyzing ΔrhlI/ΔlasI co-culture swarming across twelve mix ratios, comparing each to wild type and fitting a quadratic ratio model, writing two results CSVs and a three-panel figure.","version":"553390f7520a6266c4f2b72a4df9e450b5383ddb4ab1ed4f9a17076e7b43bde7","model":"westlakehpc/deepseek-v4.1-flash[1m]","at":"2026-11-01T17:06:12.932Z","facts":"R script, 669 lines, 11 functions","strategy":"text","cost":{"usd":0.00046038969599999994,"basis":"estimated","note":"models.dev's median price for deepseek/deepseek-v4.1-flash across 101 providers"}},"state":"described"}],"descriptionSpend":{"calls":6,"usd":0.003848802816,"estimated":6,"unknown":0},"files":{"changed":[{"path":"analysis/swarming_cocultures.R","change":"modified","modifiedAt":"2026-11-01T17:05:30.881Z","bytes":28974},{"path":"project-notes.md","change":"modified","modifiedAt":"2026-11-01T17:10:19.578Z","bytes":13424},{"path":"results/swarming_cocultures_summary.csv","change":"added","modifiedAt":"2026-11-01T17:10:44.180Z","bytes":3407},{"path":"results/swarming_cocultures_ratio_model.csv","change":"added","modifiedAt":"2026-11-01T17:10:47.403Z","bytes":4316},{"path":"results/swarming_cocultures.png","change":"added","modifiedAt":"2026-11-01T17:10:47.942Z","bytes":234096}],"omitted":0,"partial":false}}],"config":{"model":"westlakehpc/deepseek-v4.1-flash[1m]"},"acpSessionId":"eb7e3d77-aaa1-464b-be54-4b9b5b9cf987","protocolVersion":1,"adapter":{"name":"@agentclientprotocol/claude-agent-acp","version":"0.97.0"},"model":"westlakehpc/deepseek-v4.1-flash[1m]","observation":{"source":"acp","sessionId":"eb7e3d77-aaa1-464b-be54-4b9b5b9cf987","sequence":11724,"at":"2026-11-01T17:15:39.634Z","connected":false,"updates":11721,"historyUpdates":0,"omitted":24,"unrepresented":11016,"plan":null,"usage":{"at":"2026-11-01T17:11:38.990Z","origin":"live","used":127830,"size":1000000,"cost":{"amount":3.568275999999999,"currency":"USD"}},"info":null,"tools":[{"at":"2026-11-01T16:58:49.046Z","origin":"live","id":"chatcmpl-tool-b6df29e2160fba39","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:49.582Z","origin":"live","id":"chatcmpl-tool-a6a7eb5eb8fa3150","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:52.285Z","origin":"live","id":"chatcmpl-tool-beeca28f286edc05","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:53.691Z","origin":"live","id":"chatcmpl-tool-9a7f20d639074cfb","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:55.258Z","origin":"live","id":"chatcmpl-tool-84eb28f9f2610671","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T16:58:58.183Z","origin":"live","id":"chatcmpl-tool-a24d1f1b0e63b5f0","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"},{"at":"2026-11-01T17:00:32.445Z","origin":"live","id":"chatcmpl-tool-8dd6945784d8a5e5","locations":[],"tool":"mcp__rho__rho_call","outcome":"rejected"},{"at":"2026-11-01T17:00:44.975Z","origin":"live","id":"chatcmpl-tool-9bffba28deeac9f8","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:01:07.428Z","origin":"live","id":"chatcmpl-tool-92c90b4ce3d359a6","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:01:31.511Z","origin":"live","id":"chatcmpl-tool-8d498cdb0c2fbca7","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:02:19.472Z","origin":"live","id":"chatcmpl-tool-83e899c6387d50f5","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:02:33.917Z","origin":"live","id":"chatcmpl-tool-80d6d7cb2533b591","locations":[{"path":"results/swarming_cocultures_summary.csv","line":1}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:02:34.332Z","origin":"live","id":"chatcmpl-tool-b0f6d7b0f487660b","locations":[{"path":"results/swarming_cocultures_ratio_model.csv","line":1}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:02:36.332Z","origin":"live","id":"chatcmpl-tool-8f2ec59002d4b779","locations":[{"path":"results/swarming_cocultures.png","line":1}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:04:21.776Z","origin":"live","id":"chatcmpl-tool-a7717366a2c3d402","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:05:06.773Z","origin":"live","id":"chatcmpl-tool-b67503b704a95a97","locations":[{"path":"analysis/swarming_cocultures.R","line":257},{"path":"analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:12.806Z","origin":"live","id":"chatcmpl-tool-a1e0e2d1aa7e465f","locations":[{"path":"analysis/swarming_cocultures.R","line":292},{"path":"analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:18.841Z","origin":"live","id":"chatcmpl-tool-ae8cdd54746f8082","locations":[{"path":"analysis/swarming_cocultures.R","line":364},{"path":"analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:24.863Z","origin":"live","id":"chatcmpl-tool-a6d1b3c2dfab27cd","locations":[{"path":"analysis/swarming_cocultures.R","line":371},{"path":"analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:30.901Z","origin":"live","id":"chatcmpl-tool-b25c09ec1e9ffc25","locations":[{"path":"analysis/swarming_cocultures.R","line":475},{"path":"analysis/swarming_cocultures.R"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:05:38.426Z","origin":"live","id":"chatcmpl-tool-b8151231bba7b10e","locations":[],"tool":"mcp__rho__rho_call","outcome":"returned","operation":"kernel.run"},{"at":"2026-11-01T17:05:43.004Z","origin":"live","id":"chatcmpl-tool-8d7ce51e52a0c488","locations":[],"tool":"Bash","outcome":"returned"},{"at":"2026-11-01T17:06:33.198Z","origin":"live","id":"chatcmpl-tool-a31f6867366b5a60","locations":[{"path":"project-notes.md","line":55}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:07:09.092Z","origin":"live","id":"chatcmpl-tool-afa93163df2807bd","locations":[{"path":"project-notes.md","line":59},{"path":"project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:07:13.784Z","origin":"live","id":"chatcmpl-tool-91469059f68c4d4a","locations":[{"path":"project-notes.md","line":48}],"tool":"Read","outcome":"returned"},{"at":"2026-11-01T17:07:33.151Z","origin":"live","id":"chatcmpl-tool-98f42ffae1befa60","locations":[{"path":"project-notes.md","line":64},{"path":"project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:07:35.182Z","origin":"live","id":"chatcmpl-tool-a549f5938b4d60ee","locations":[{"path":"project-notes.md","line":65},{"path":"project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:07:37.204Z","origin":"live","id":"chatcmpl-tool-87ae6a2c21aa0238","locations":[{"path":"project-notes.md","line":76},{"path":"project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:08:17.319Z","origin":"live","id":"chatcmpl-tool-8cb7dc915ddc4fa2","locations":[{"path":"project-notes.md","line":64},{"path":"project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:10:19.593Z","origin":"live","id":"chatcmpl-tool-8de2edd619034840","locations":[{"path":"project-notes.md","line":64},{"path":"project-notes.md"}],"tool":"Edit","outcome":"returned"},{"at":"2026-11-01T17:10:47.974Z","origin":"live","id":"chatcmpl-tool-beb256a58642eedc","locations":[],"tool":"Bash","outcome":"returned"},{"at":"2026-11-01T17:10:54.634Z","origin":"live","id":"chatcmpl-tool-8c51cf1fcd7e00fc","locations":[],"tool":"mcp__rho__rho_read","outcome":"returned"}],"config":{"at":"2026-11-01T16:56:10.108Z","origin":"initial","options":[{"id":"mode","name":"Mode","category":"mode","description":"Session permission mode","type":"select","current":"default","values":[{"value":"default","name":"Manual","description":"Always ask before making changes"},{"value":"acceptEdits","name":"Accept edits","description":"Automatically accept all file edits"},{"value":"plan","name":"Plan","description":"Create a plan before making changes"},{"value":"auto","name":"Auto","description":"Claude handles permission decisions"},{"value":"bypassPermissions","name":"Bypass permissions","description":"Accepts all permissions"}]},{"id":"model","name":"Model","category":"model","description":"AI model to use","type":"select","current":"westlakehpc/deepseek-v4.1-flash[1m]","values":[{"value":"westlakehpc/deepseek-v4.1-flash[1m]","name":"DeepSeek V4.1 Flash"}]},{"id":"effort","name":"Effort","category":"thought_level","description":"Available effort levels for this model","type":"select","current":"xhigh","values":[{"value":"default","name":"Default"},{"value":"low","name":"Low"},{"value":"medium","name":"Medium"},{"value":"high","name":"High"},{"value":"xhigh","name":"Xhigh"},{"value":"max","name":"Max"}]},{"id":"ultracode","name":"Ultracode","category":"model_config","description":"Dynamic workflows on every task, at any effort level","type":"select","current":"off","values":[{"value":"on","name":"On"},{"value":"off","name":"Off"}]}],"omitted":0}}}