diff --git a/Dockerfile b/Dockerfile index 2145d8e2..c5cee784 100644 --- a/Dockerfile +++ b/Dockerfile @@ -133,9 +133,9 @@ RUN AUTO_UPDATE=1 conda install --no-update-deps -y \ # Tier 2: tools with regular updates (2-4/year) RUN AUTO_UPDATE=1 conda install --no-update-deps -y \ -c daemontus \ - biodivine_aeon=1.2.0=py311h9bf148f_0 \ + biodivine_aeon=1.2.3=py311h9bf148f_0 \ maboss=2.6.0=he9e06a5_1 \ - pyboolnet=3.0.14=py311_0 \ + pyboolnet=3.0.16=py311_0 \ && conda clean -y --all && rm -rf /opt/conda/pkgs # Tier 3: tools with frequent updates (>4/year) or lightweight with thin dependencies @@ -144,12 +144,12 @@ RUN AUTO_UPDATE=1 conda install --no-update-deps -y \ algorecell_types=1.0=py_0 \ bns-python=0.2=py_0 \ bonesis=0.6.7=py_0 \ - boon=1.26=py_0 \ + boon=1.28=py_0 \ boolsim-python=0.5=py_0 \ cabean-python=1.0=py_0 \ caspo-control=1.0=py_0 \ casq=1.3.3=pyhd8ed1ab_0 \ - colomoto_jupyter=0.8.9=py_0 \ + colomoto_jupyter=0.8.11=py_0 \ ginsim-python=0.4.5=py_0 \ mpbn=3.8=py_0 \ nordic=2.5.0=py_0 \ diff --git a/docs/_toc.yml b/docs/_toc.yml index a0a5f754..5591d164 100644 --- a/docs/_toc.yml +++ b/docs/_toc.yml @@ -76,6 +76,9 @@ parts: - file: tools/pyboolnet sections: - glob: tutorials/[pP][yY][bB][oO][oO][lL][nN][eE][tT]/* + - file: tools/pydruglogics + sections: + - glob: tutorials/[pP][yY][dD][rR][uU][gG][lL][oO][gG][iI][cC][sS]/* - file: tools/pystablemotifs sections: - glob: tutorials/[pP][yY][sS][tT][aA][bB][lL][eE][mM][oO][tT][iI][fF][sS]/* diff --git a/hooks/release_changes.json b/hooks/release_changes.json index b6055a36..393f5079 100644 --- a/hooks/release_changes.json +++ b/hooks/release_changes.json @@ -124,6 +124,11 @@ "description": "Generation, modification and analysis of Boolean networks", "release_url": "https://github.com/hklarner/PyBoolNet/releases/tag/v{}" }, + "pydruglogics": { + "name": "PyDrugLogics", + "description": "Construct, optimize Boolean Models and perform in-silico perturbations of the models", + "release_url": "https://github.com/druglogics/pydruglogics/releases/tag/v{}" + }, "pymaboss": { "name": "PyMaBoSS", "description": "Python interface to MaBoSS", diff --git a/tools/index.md b/tools/index.md index c1c08918..08373161 100644 --- a/tools/index.md +++ b/tools/index.md @@ -25,6 +25,7 @@ The CoLoMoTo Docker image provides access to the following softwares: | NuSMV | http://nusmv.fbk.eu | Symbolic model-checker | Python module [`nusmv`](https://github.com/colomoto/colomoto-jupyter) | | Pint | https://loicpauleve.name/pint | Static analyzer for dynamics of Automata Networks | Python module [`pypint`](https://github.com/pauleve/pypint) | | PyBoolNet | https://github.com/hklarner/PyBoolNet | Generation, modification and analysis of Boolean networks | Python module [`PyBoolNet`](https://github.com/hklarner/PyBoolNet) | +| PyDrugLogics | https://druglogics.github.io/pydruglogics/ | Construct, optimize Boolean Models and perform in-silico perturbations of the models | Python module [`pydruglogics`](https://druglogics.github.io/pydruglogics/api.html) | | pyStableMotifs | https://github.com/jcrozum/pystablemotifs | Target-control of Boolean networks | Python module [`pystablemotifs`](https://github.com/jcrozum/pystablemotifs) | | R-BoolNet | https://cran.r-project.org/package=BoolNet | Analysis and reconstruction of Boolean networks dynamics | RPY2 python interface | | scBoolSeq | https://github.com/bnediction/scBoolSeq | scRNA-Seq data binarisation and synthetic generation from Boolean dynamics | Python module [`scboolseq`](https://github.com/bnediction/scBoolSeq) |