edkerk · Oct 17, 2026 · Oct 17, 2026 · Oct 17, 2026
diff --git a/.gitmodules b/.gitmodules
@@ -1,11 +1,11 @@
 [submodule "RAVEN"]
 	path = RAVEN
-	url = https://github.com/SysBioChalmers/RAVEN.git
-	branch = develop3
+	url = https://github.com/CompMetEng/RAVEN.git
+	branch = develop
 	shallow = true
 [submodule "raven-toolbox"]
 	path = raven-toolbox
-	url = https://github.com/SysBioChalmers/raven-toolbox.git
+	url = https://github.com/CompMetEng/raven-toolbox.git
 	branch = develop
 	shallow = true
 [submodule "hanpo-GEM"]

diff --git a/RAVEN b/RAVEN
diff --git a/README.md b/README.md
@@ -15,10 +15,10 @@ The site combines:
 - a complete, worked **GEM reconstruction protocol** (the *Hansenula
   polymorpha* `hanpo-GEM` example).
 
-The source repositories are tracked as git submodules pinned to their `main`
-branches: [`RAVEN`](https://github.com/SysBioChalmers/RAVEN),
-[`raven-toolbox`](https://github.com/SysBioChalmers/raven-toolbox) and
-[`hanpo-GEM`](https://github.com/SysBioChalmers/hanpo-GEM).
+The source repositories are tracked as git submodules that follow the branches
+set in `.gitmodules`: [`RAVEN`](https://github.com/CompMetEng/RAVEN) and
+[`raven-toolbox`](https://github.com/CompMetEng/raven-toolbox) at `develop`, and
+[`hanpo-GEM`](https://github.com/SysBioChalmers/hanpo-GEM) at `main`.
 
 ## Building locally
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -10,7 +10,7 @@
 from __future__ import annotations
 
 project = "RAVEN"
-copyright = "SysBioChalmers"
+copyright = "CompMetEng"
 author = "Wang, Marcisauskas, Sanchez, Domenzain, Hermansson, Agren, Nielsen, Kerkhoven et al."
 
 extensions = [
@@ -60,13 +60,13 @@
     "icon_links": [
         {
             "name": "RAVEN (MATLAB) on GitHub",
-            "url": "https://github.com/SysBioChalmers/RAVEN",
+            "url": "https://github.com/CompMetEng/RAVEN",
             "icon": "fa-brands fa-github",
             "type": "fontawesome",
         },
         {
             "name": "raven-toolbox (Python) on GitHub",
-            "url": "https://github.com/SysBioChalmers/raven-toolbox",
+            "url": "https://github.com/CompMetEng/raven-toolbox",
             "icon": "fa-brands fa-github",
             "type": "fontawesome",
         },

diff --git a/docs/guide/combining.md b/docs/guide/combining.md
@@ -285,7 +285,7 @@ information and should go; an **exchange** had a single metabolite all along
 (`=> glucose`) and must be kept. raven-toolbox used to delete those too,
 along with the objective, taking this model from growth `0.1222` to `0.0000`
 with no error and no warning. Fixed in
-[raven-toolbox#96](https://github.com/SysBioChalmers/raven-toolbox/pull/96);
+[raven-toolbox#96](https://github.com/CompMetEng/raven-toolbox/pull/96);
 if a flattened model comes back with no boundary reactions, update
 raven-toolbox.
 :::

diff --git a/docs/index.md b/docs/index.md
@@ -27,14 +27,14 @@ Then run `checkRaven` to verify.
 :::{tab-item} Python (git)
 
 ```bash
-git clone --depth=1 https://github.com/SysBioChalmers/raven-toolbox.git
+git clone --depth=1 https://github.com/CompMetEng/raven-toolbox.git
 pip install -e raven-toolbox/
 ```
 :::
 :::{tab-item} MATLAB (git)
 
 ```bash
-git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git
+git clone --depth=1 https://github.com/CompMetEng/RAVEN.git
 ```
 
 Add the folder to the MATLAB path, then run `checkRaven` to verify.
@@ -171,20 +171,20 @@ RAVEN paper and the GEM reconstruction protocol.
 ## Source code
 
 RAVEN is publicly available under the GPLv3 license at
-[SysBioChalmers/RAVEN](https://github.com/SysBioChalmers/RAVEN){.github},
+[CompMetEng/RAVEN](https://github.com/CompMetEng/RAVEN){.github},
 archived at
 [https://doi.org/10.5281/zenodo.3689518](https://doi.org/10.5281/zenodo.3689518).
 raven-toolbox, the Python port, is under the MIT license at
-[SysBioChalmers/raven-toolbox](https://github.com/SysBioChalmers/raven-toolbox){.github}.
+[CompMetEng/raven-toolbox](https://github.com/CompMetEng/raven-toolbox){.github}.
 
 ## Issues and discussions
 
 Report a bug or request a feature on the tracker for the toolbox it concerns:
-[RAVEN issues](https://github.com/SysBioChalmers/RAVEN/issues){.github} for the
-MATLAB toolbox, [raven-toolbox issues](https://github.com/SysBioChalmers/raven-toolbox/issues){.github}
+[RAVEN issues](https://github.com/CompMetEng/RAVEN/issues){.github} for the
+MATLAB toolbox, [raven-toolbox issues](https://github.com/CompMetEng/raven-toolbox/issues){.github}
 for the Python package. For questions and general discussion, use
-[RAVEN discussions](https://github.com/SysBioChalmers/RAVEN/discussions){.github}
-or [raven-toolbox discussions](https://github.com/SysBioChalmers/raven-toolbox/discussions){.github}.
+[RAVEN discussions](https://github.com/CompMetEng/RAVEN/discussions){.github}
+or [raven-toolbox discussions](https://github.com/CompMetEng/raven-toolbox/discussions){.github}.
 
 ```{toctree}
 :hidden:

diff --git a/docs/installation/data-and-binaries.md b/docs/installation/data-and-binaries.md
@@ -6,7 +6,7 @@ fetched on first use from a shared, checksummed release and cached locally. This
 page covers what is fetched, where it is kept, and how to override each step.
 
 Both toolboxes read from the same
-[`raven-data`](https://github.com/SysBioChalmers/raven-data) repository, so the
+[`toolbox-assets`](https://github.com/CompMetEng/toolbox-assets) repository, so the
 files RAVEN downloads and the files raven-toolbox downloads are the same files.
 
 ## What gets downloaded

diff --git a/docs/installation/python.md b/docs/installation/python.md
@@ -40,7 +40,7 @@ pip install raven-toolbox
 For the latest unreleased code or to contribute:
 
 ```bash
-git clone https://github.com/SysBioChalmers/raven-toolbox.git
+git clone https://github.com/CompMetEng/raven-toolbox.git
 cd raven-toolbox
 pip install -e .
 ```

diff --git a/docs/installation/raven.md b/docs/installation/raven.md
@@ -1,9 +1,7 @@
 # RAVEN (MATLAB)
 
 The RAVEN Toolbox runs in MATLAB and works completely independently; it does
-not require the COBRA Toolbox, although it can interoperate with it. The
-canonical reference is the
-[RAVEN installation wiki](https://github.com/SysBioChalmers/RAVEN/wiki/Installation).
+not require the COBRA Toolbox, although it can interoperate with it.
 
 ## Requirements
 
@@ -103,12 +101,12 @@ If MATLAB does not pick up the toolbox after step 2, run
 :::{tab-item} {octicon}`download;1em` Release download
 
 Good for offline or managed environments. **The
-[RAVEN releases page](https://github.com/SysBioChalmers/RAVEN/releases)
+[RAVEN releases page](https://github.com/CompMetEng/RAVEN/releases)
 itself only lists stable releases**; 3.0.0b1 is a git tag with no packaged
 release, so download it directly instead:
 
 1. Download
-   [the 3.0.0b1 archive](https://github.com/SysBioChalmers/RAVEN/archive/refs/tags/3.0.0b1.zip)
+   [the 3.0.0b1 archive](https://github.com/CompMetEng/RAVEN/archive/refs/tags/3.0.0b1.zip)
    directly (this works without git).
 2. Extract it to a location of your choice.
 3. In MATLAB, add the RAVEN folder to the path (`pathtool`), then
@@ -117,11 +115,11 @@ release, so download it directly instead:
 :::{tab-item} {octicon}`git-branch;1em` Clone with git
 
 Clones the repository, then checks out the `3.0.0b1` tag specifically: a
-plain `git clone` alone tracks the `main` branch (stable RAVEN 2), not this
-site's pre-release.
+plain `git clone` alone tracks the `develop` branch, which can contain changes
+made after this site's pre-release.
 
 ```bash
-git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git
+git clone --depth=1 https://github.com/CompMetEng/RAVEN.git
 cd RAVEN
 git fetch --depth=1 origin tag 3.0.0b1
 git checkout 3.0.0b1
@@ -253,6 +251,5 @@ Then delete the cloned RAVEN folder from disk.
 
 ## Getting help
 
-For installation problems, consult the
-[RAVEN wiki](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) or
-open an issue on [GitHub](https://github.com/SysBioChalmers/RAVEN/issues).
+For installation problems, open an issue on
+[GitHub](https://github.com/CompMetEng/RAVEN/issues).
diff --git a/docs/parameter-tuning/studies/init-param-calibration.md b/docs/parameter-tuning/studies/init-param-calibration.md
@@ -200,7 +200,7 @@ nothing to reconcile, but the values rest on convention rather than evidence.
 ## 4. Cross-solver portability
 
 See [init-solver-benchmark.md](init-solver-benchmark.md) for the genome-scale
-solver comparison (Gurobi/HiGHS/GLPK) and [tests/test_init_solvers.py](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/tests/test_init_solvers.py)
+solver comparison (Gurobi/HiGHS/GLPK) and [tests/test_init_solvers.py](https://github.com/CompMetEng/raven-toolbox/blob/develop/tests/test_init_solvers.py)
 for CI parameterised over installed MILP backends. Summary: at genome scale only Gurobi
 is viable today; HiGHS fails on an upstream optlang `hybrid_interface.clone()` bug; GLPK
 ignores `configuration.timeout` on MIP and ran 1 h+ without converging. Toy-scale

diff --git a/docs/parameter-tuning/studies/kegg-hmm-cutoff-calibration.md b/docs/parameter-tuning/studies/kegg-hmm-cutoff-calibration.md
@@ -29,7 +29,7 @@ in three steps:
   recall = |pred ∩ truth| / |truth|, F1. Reaction-level: `rxn_rec` = fraction of
   the organism's true reactions recovered (KO→reaction via `ko_reaction`);
   `rxn_novel` = predicted reactions **not** in the annotation set.
-- Reproduce with [`scripts/analyze_hmm_cutoffs.py`](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/scripts/analyze_hmm_cutoffs.py).
+- Reproduce with [`scripts/analyze_hmm_cutoffs.py`](https://github.com/CompMetEng/raven-toolbox/blob/develop/scripts/analyze_hmm_cutoffs.py).
 
 ### Important caveat
 

diff --git a/docs/parameter-tuning/studies/sampling-convergence-calibration.md b/docs/parameter-tuning/studies/sampling-convergence-calibration.md
@@ -44,7 +44,7 @@ convergence threshold) or > 1.01 (the stricter one used in published MCMC
 work) flags a reaction whose distribution still depends on where its chain
 started.
 
-* Driver: [`scripts/analyze_sampling_convergence.py`](https://github.com/SysBioChalmers/raven-toolbox/blob/docs/parameter-defaults/scripts/analyze_sampling_convergence.py)
+* Driver: [`scripts/analyze_sampling_convergence.py`](https://github.com/CompMetEng/raven-toolbox/blob/docs/parameter-defaults/scripts/analyze_sampling_convergence.py)
 * Settings matched to the existing single-chain study for direct comparison:
   `n_samples=300`, `thinning=100`, `warmup=1000` (cobrapy/RAVEN defaults).
 * `n_chains=4`, run in parallel via `ProcessPoolExecutor` (one process per

diff --git a/docs/protocol/materials.md b/docs/protocol/materials.md
@@ -9,7 +9,7 @@ Most of it is open source or available under an academic license.
 | Software | Dependency | Source |
 |---|---|---|
 | MATLAB | License | <https://mathworks.com/products/matlab.html> |
-| RAVEN | libSBML, solver | <https://github.com/SysBioChalmers/RAVEN> |
+| RAVEN | libSBML, solver | <https://github.com/CompMetEng/RAVEN> |
 | COBRA | MATLAB | <https://github.com/opencobra/cobratoolbox> |
 | Gurobi | License | <https://www.gurobi.com/products/gurobi-optimizer/> |
 | libSBML | MATLAB | <http://sbml.org/Software/libSBML> |
@@ -78,5 +78,5 @@ successful run looks like.
 If `checkRaven` reports that importing SBML format **failed**, uninstall
 MATLAB's **Text Analytics Toolbox**, which conflicts with RAVEN's Excel
 parser. For support, see the
-[RAVEN issues](https://github.com/SysBioChalmers/RAVEN/issues) page.
+[RAVEN issues](https://github.com/CompMetEng/RAVEN/issues) page.
 :::
diff --git a/docs/raven3-migration.md b/docs/raven3-migration.md
@@ -28,7 +28,7 @@ RAVEN 3 is a deliberate breaking release: the codebase was reorganized, a large
 number of low-value or duplicate functions were removed, several external
 dependencies were dropped, and the calling convention for optional function
 arguments changed almost everywhere. None of this was accidental; see the
-project's [v3 development review](https://github.com/SysBioChalmers/RAVEN/blob/develop3/docs/v3_review.md)
+project's [v3 development review](https://github.com/CompMetEng/RAVEN/blob/develop/docs/v3_review.md)
 for the rationale, but it means that **most non-trivial RAVEN 2 scripts need to
 be checked**, even though the core reconstruction and analysis behavior is
 mostly the same.

diff --git a/docs/tuned-parameters.md b/docs/tuned-parameters.md
@@ -175,7 +175,7 @@ still changing.
 **Full detail:** the measurements behind these values (the yeast-GEM benchmark,
 the head-to-head against MATLAB's `predictLocalization`, the predictor
 benchmarks across four organisms, and the design documents) are in
-[raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity/tree/develop/docs/localization),
+[raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity/tree/develop/docs/localization),
 with the rest of the work in progress on this method.
 
 ## Model manipulation

diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
@@ -10,7 +10,7 @@ the exercises themselves are otherwise unchanged. They use the **MATLAB**
 toolbox and build up from running a simulation on an existing model to
 reconstructing a genome-scale model from sequence data. The scripts and all the
 data files they use live in the
-[`tutorial/`](https://github.com/SysBioChalmers/RAVEN/tree/main/tutorial)
+[`tutorial/`](https://github.com/CompMetEng/RAVEN/tree/develop/tutorial)
 folder of the RAVEN repository.
 
 | # | Tutorial | What you learn |

diff --git a/docs/yaml-format.md b/docs/yaml-format.md
@@ -4,7 +4,7 @@ This document describes the YAML format produced and consumed by
 
 - **cobrapy** ([`cobra.io.{load,save}_yaml_model`](https://github.com/opencobra/cobrapy))
 - **raven-toolbox** (`raven_toolbox.io.yaml.{read,write}_yaml_model`, see [API](api/index.md))
-- **RAVEN MATLAB** (`readYAMLmodel.m` / `writeYAMLmodel.m` in the [RAVEN repo](https://github.com/SysBioChalmers/RAVEN/tree/develop3/io))
+- **RAVEN MATLAB** (`readYAMLmodel.m` / `writeYAMLmodel.m` in the [RAVEN repo](https://github.com/CompMetEng/RAVEN/tree/develop/io))
 
 The same file can be round-tripped through any of the three. cobrapy is the canonical core; raven-toolbox and RAVEN MATLAB add namespaced extensions (RAVEN curation fields, MIRIAM cross-refs already covered by cobrapy's `annotation`, and the GECKO `ec-*` sections) without disturbing the cobra-known shape.
 
@@ -296,7 +296,7 @@ In a double-quoted string, only `\` and `"` are escaped. Other characters (inclu
 
 "Full" = every field read back into its canonical position on the model object; "core" = cobrapy-known fields, RAVEN extensions ignored or kept on the object as attribute fall-through (`reaction.eccodes` etc., not re-emitted on save). A round-trip through cobrapy is therefore **lossy for RAVEN extensions**: only the core fields survive `cobrapy.load → cobrapy.save`. Round-trips through raven-toolbox or RAVEN MATLAB are lossless.
 
-Neither writer reproduces cobrapy's own `ruamel`-default layout byte-for-byte (indentation, quoting style, line folding); RAVEN and raven-toolbox instead share a layout with each other, close to cobrapy's structural shape but not identical to it. See [raven-gecko-parity's reconciliation record](https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/yaml-reconciliation.md) for why, and for the one scenario (`yaml_roundtrip_smallyeast`) that continuously checks the two writers agree.
+Neither writer reproduces cobrapy's own `ruamel`-default layout byte-for-byte (indentation, quoting style, line folding); RAVEN and raven-toolbox instead share a layout with each other, close to cobrapy's structural shape but not identical to it. See [raven-gecko-parity's reconciliation record](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/yaml-reconciliation.md) for why, and for the one scenario (`yaml_roundtrip_smallyeast`) that continuously checks the two writers agree.
 
 ---
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -4,8 +4,8 @@ site_description: >-
   Toolbox (MATLAB) and raven-toolbox, documented side by side.
 site_author: Wang, Marcisauskas, Sanchez, Domenzain, Hermansson, Agren, Nielsen, Kerkhoven et al.
 site_url: https://raven-docs.readthedocs.io/en/latest/
-repo_url: https://github.com/SysBioChalmers/RAVEN
-repo_name: SysBioChalmers/RAVEN
+repo_url: https://github.com/CompMetEng/RAVEN
+repo_name: CompMetEng/RAVEN
 edit_uri: ""
 
 # Build-time hooks that keep the site resilient to structural changes in the