Getting Started

Installation

To install MOSNA for use with GPU compatible libraries:

conda create --solver=libmamba -n mosna-gpu -c rapidsai -c conda-forge -c nvidia -c pytorch rapids=23.04.01 python=3.10 cuda-version=11.2 pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 scanpy
conda activate mosna-gpu

Alternatively without GPU:

conda create --solver=libmamba -n mosna -c conda-forge python=3.10 scanpy
conda activate mosna

Then, install some essential dependencies:

pip install ipykernel ipywidgets
pip install tysserand
pip install -e .
pip install scipy==1.13

Alternatively, you can create a new Conda environment that has tysserand, mosna and all their dependencies installed:

conda env create -f mosna.yml

or copy the YAML content directly:

name: mosna-survival
channels:
  - defaults
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - anndata=0.11.4=pyhd8ed1ab_0
  - arpack=3.9.1=nompi_hf03ea27_102
  - array-api-compat=1.12.0=pyhe01879c_0
  - brotli=1.2.0=h41a2e66_0
  - brotli-bin=1.2.0=hf2c8021_0
  - bzip2=1.0.8=hda65f42_8
  - c-ares=1.34.5=hb9d3cd8_0
  - ca-certificates=2025.11.12=hbd8a1cb_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - colorama=0.4.6=pyhd8ed1ab_1
  - colorcet=3.1.0=pyhd8ed1ab_1
  - contourpy=1.3.2=py310h3788b33_0
  - cycler=0.12.1=pyhd8ed1ab_1
  - ecos=2.0.14=np2py310h99de88f_3
  - exceptiongroup=1.3.0=pyhd8ed1ab_0
  - fonttools=4.60.1=py310h3406613_0
  - freetype=2.14.1=ha770c72_0
  - glpk=5.0=h445213a_0
  - gmp=6.3.0=hac33072_2
  - h5py=3.15.1=nompi_py310h4aa865e_100
  - hdf5=1.14.6=nompi_h6e4c0c1_103
  - icu=75.1=he02047a_0
  - igraph=1.0.0=hfe3e89f_0
  - joblib=1.5.2=pyhd8ed1ab_0
  - keyutils=1.6.3=hb9d3cd8_0
  - kiwisolver=1.4.9=py310haaf941d_2
  - krb5=1.21.3=h659f571_0
  - lcms2=2.17=h717163a_0
  - ld_impl_linux-64=2.45=h1aa0949_0
  - legacy-api-wrap=1.5=pyhd8ed1ab_0
  - leidenalg=0.11.0=py310hea6c23e_0
  - lerc=4.0.0=h0aef613_1
  - libaec=1.1.4=h3f801dc_0
  - libblas=3.9.0=39_h4a7cf45_openblas
  - libbrotlicommon=1.2.0=h09219d5_0
  - libbrotlidec=1.2.0=hd53d788_0
  - libbrotlienc=1.2.0=h02bd7ab_0
  - libcblas=3.9.0=39_h0358290_openblas
  - libcurl=8.17.0=h4e3cde8_0
  - libdeflate=1.25=h17f619e_0
  - libedit=3.1.20250104=pl5321h7949ede_0
  - libev=4.33=hd590300_2
  - libexpat=2.7.1=hecca717_0
  - libffi=3.5.2=h9ec8514_0
  - libfreetype=2.14.1=ha770c72_0
  - libfreetype6=2.14.1=h73754d4_0
  - libgcc=15.2.0=h767d61c_7
  - libgcc-ng=15.2.0=h69a702a_7
  - libgfortran=15.2.0=h69a702a_7
  - libgfortran5=15.2.0=hcd61629_7
  - libgomp=15.2.0=h767d61c_7
  - libhwloc=2.12.1=default_h7f8ec31_1002
  - libiconv=1.18=h3b78370_2
  - libjpeg-turbo=3.1.2=hb03c661_0
  - liblapack=3.9.0=39_h47877c9_openblas
  - libleidenalg=0.12.0=hb700be7_0
  - liblzma=5.8.1=hb9d3cd8_2
  - libnghttp2=1.67.0=had1ee68_0
  - libnsl=2.0.1=hb9d3cd8_1
  - libopenblas=0.3.30=pthreads_h94d23a6_4
  - libosqp=0.6.3=h5888daf_1
  - libpng=1.6.50=h421ea60_1
  - libqdldl=0.1.7=hcb278e6_0
  - libsqlite=3.51.0=hee844dc_0
  - libssh2=1.11.1=hcf80075_0
  - libstdcxx=15.2.0=h8f9b012_7
  - libstdcxx-ng=15.2.0=h4852527_7
  - libtiff=4.7.1=h9d88235_1
  - libuuid=2.41.2=he9a06e4_0
  - libwebp-base=1.6.0=hd42ef1d_0
  - libxcb=1.17.0=h8a09558_0
  - libxcrypt=4.4.36=hd590300_1
  - libxgboost=3.1.1=cpu_h2ebb00f_0
  - libxml2=2.15.1=h26afc86_0
  - libxml2-16=2.15.1=ha9997c6_0
  - libxml2-devel=2.15.1=h26afc86_0
  - libzlib=1.3.1=hb9d3cd8_2
  - llvmlite=0.45.1=py310hee1c697_0
  - matplotlib-base=3.10.8=py310hfde16b3_0
  - munkres=1.1.4=pyhd8ed1ab_1
  - natsort=8.4.0=pyh29332c3_1
  - ncurses=6.5=h2d0b736_3
  - networkx=3.4.2=pyh267e887_2
  - nomkl=1.0=h5ca1d4c_0
  - numba=0.62.1=py310h3477d8a_0
  - numexpr=2.14.1=py310h34a7263_101
  - openjpeg=2.5.4=h55fea9a_0
  - openssl=3.6.0=h26f9b46_0
  - osqp=0.6.7.post3=py310h5eaa309_1
  - packaging=25.0=pyh29332c3_1
  - pandas=2.3.3=py310h0158d43_1
  - patsy=1.0.2=pyhcf101f3_0
  - pillow=12.0.0=py310h80abafc_0
  - pip=25.3=pyh8b19718_0
  - pthread-stubs=0.4=hb9d3cd8_1002
  - py-xgboost=3.1.1=cpu_pyh35227d3_0
  - pynndescent=0.5.13=pyhd8ed1ab_1
  - pyparsing=3.2.5=pyhcf101f3_0
  - python=3.10.19=h3c07f61_2_cpython
  - python-dateutil=2.9.0.post0=pyhe01879c_2
  - python-igraph=1.0.0=py310hea6c23e_0
  - python-tzdata=2025.2=pyhd8ed1ab_0
  - python_abi=3.10=8_cp310
  - pytz=2025.2=pyhd8ed1ab_0
  - qdldl-python=0.1.7.post5=np20py310h5ebf739_1
  - qhull=2020.2=h434a139_5
  - readline=8.2=h8c095d6_2
  - scanpy=1.11.5=pyhd8ed1ab_0
  - scikit-learn=1.7.2=py310h228f341_0
  - scikit-survival=0.25.0=np2py310h99cdc5b_0
  - seaborn=0.13.2=hd8ed1ab_3
  - seaborn-base=0.13.2=pyhd8ed1ab_3
  - session-info2=0.2.3=pyhd8ed1ab_0
  - setuptools=80.9.0=pyhff2d567_0
  - six=1.17.0=pyhe01879c_1
  - statsmodels=0.14.5=py310hf779ad0_1
  - tbb=2022.3.0=h8d10470_1
  - texttable=1.7.0=pyhd8ed1ab_1
  - threadpoolctl=3.6.0=pyhecae5ae_0
  - tk=8.6.13=noxft_ha0e22de_103
  - tqdm=4.67.1=pyhd8ed1ab_1
  - typing-extensions=4.15.0=h396c80c_0
  - typing_extensions=4.15.0=pyhcf101f3_0
  - tzdata=2025b=h78e105d_0
  - umap-learn=0.5.9.post2=py310hff52083_0
  - unicodedata2=17.0.0=py310h7c4b9e2_1
  - wheel=0.45.1=pyhd8ed1ab_1
  - xgboost=3.1.1=cpu_pyhb39878e_0
  - xorg-libxau=1.0.12=hb03c661_1
  - xorg-libxdmcp=1.1.5=hb03c661_1
  - zlib-ng=2.2.5=hde8ca8f_0
  - zstd=1.5.7=hb8e6e7a_2
  - pip:
      - aiohappyeyeballs==2.6.1
      - aiohttp==3.13.2
      - aiosignal==1.4.0
      - alabaster==1.0.0
      - annotated-types==0.7.0
      - annoy==1.17.3
      - app-model==0.4.0
      - appdirs==1.4.4
      - asciitree==0.3.3
      - asttokens==3.0.1
      - async-timeout==5.0.1
      - attrs==25.4.0
      - autograd==1.8.0
      - autograd-gamma==0.5.0
      - babel==2.17.0
      - bermuda==0.1.6
      - bokeh==3.8.1
      - build==1.3.0
      - cachey==0.2.1
      - certifi==2025.11.12
      - charset-normalizer==3.4.4
      - click==8.3.1
      - cloudpickle==3.1.2
      - comm==0.2.3
      - composition-stats==2.0.0
      - dask==2025.11.0
      - debugpy==1.8.17
      - decorator==5.2.1
      - distributed==2025.11.0
      - docstring-parser==0.17.0
      - docutils==0.21.2
      - executing==2.2.1
      - fasteners==0.20
      - fbpca==1.0
      - flexcache==0.3
      - flexparser==0.4
      - formulaic==1.2.1
      - freetype-py==2.5.1
      - frozenlist==1.8.0
      - fsspec==2025.10.0
      - geosketch==1.3
      - hdbscan==0.8.40
      - heapdict==1.0.1
      - hsluv==5.0.4
      - idna==3.11
      - imageio==2.37.2
      - imagesize==1.4.1
      - importlib-metadata==8.7.0
      - in-n-out==0.2.1
      - interface-meta==1.3.0
      - intervaltree==3.1.0
      - ipykernel==6.31.0
      - ipython==8.37.0
      - ipython-pygments-lexers==1.1.1
      - ipywidgets==8.1.8
      - jedi==0.19.2
      - jinja2==3.1.6
      - jsonschema==4.25.1
      - jsonschema-specifications==2025.9.1
      - jupyter-client==8.6.3
      - jupyter-core==5.9.1
      - jupyterlab-widgets==3.0.16
      - lazy-loader==0.4
      - lifelines==0.30.0
      - lightkit==0.5.0
      - lightning-utilities==0.15.2
      - locket==1.0.0
      - lz4==4.4.5
      - magicgui==0.10.1
      - markdown-it-py==4.0.0
      - markupsafe==3.0.3
      - matplotlib-inline==0.2.1
      - mdurl==0.1.2
      - msgpack==1.1.2
      - multidict==6.7.0
      - napari==0.6.6
      - napari-console==0.1.4
      - napari-plugin-engine==0.2.0
      - napari-plugin-manager==0.1.8
      - napari-svg==0.2.1
      - narwhals==2.11.0
      - nest-asyncio==1.6.0
      - npe2==0.7.9
      - numcodecs==0.13.1
      - numpy==1.26.4
      - numpydoc==1.9.0
      - opencv-python-headless==4.12.0.88
      - parso==0.8.5
      - partd==1.4.2
      - pathlib==1.0.1
      - pexpect==4.9.0
      - pint==0.24.4
      - platformdirs==4.5.0
      - pooch==1.8.2
      - prompt-toolkit==3.0.52
      - propcache==0.4.1
      - psutil==7.1.3
      - psygnal==0.15.0
      - ptyprocess==0.7.0
      - pure-eval==0.2.3
      - pyarrow==22.0.0
      - pycave==3.2.1
      - pyconify==0.2.1
      - pydantic==2.12.4
      - pydantic-compat==0.1.2
      - pydantic-core==2.41.5
      - pygments==2.19.2
      - pyopengl==3.1.10
      - pyproject-hooks==1.2.0
      - pyqt5==5.15.11
      - pyqt5-qt5==5.15.18
      - pyqt5-sip==12.17.1
      - pytorch-lightning==1.9.5
      - pyyaml==6.0.3
      - pyzmq==27.1.0
      - qtconsole==5.7.0
      - qtpy==2.4.3
      - referencing==0.37.0
      - requests==2.32.5
      - rich==14.2.0
      - rpds-py==0.29.0
      - scanorama==1.7.4
      - scikit-image==0.25.2
      - scipy==1.13.0
      - shellingham==1.5.4
      - snowballstemmer==3.0.1
      - sortedcontainers==2.4.0
      - sphinx==8.1.3
      - sphinxcontrib-applehelp==2.0.0
      - sphinxcontrib-devhelp==2.0.0
      - sphinxcontrib-htmlhelp==2.1.0
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-qthelp==2.0.0
      - sphinxcontrib-serializinghtml==2.0.0
      - stack-data==0.6.3
      - superqt==0.7.6
      - tblib==3.2.2
      - tifffile==2025.5.10
      - tomli==2.3.0
      - tomli-w==1.2.0
      - toolz==1.1.0
      - torch==1.12.1
      - torchmetrics==0.11.4
      - tornado==6.5.2
      - traitlets==5.14.3
      - triangle==20250106
      - typer==0.20.0
      - typing-inspection==0.4.2
      - tysserand==0.6.0
      - urllib3==2.5.0
      - vispy==0.15.2
      - wcwidth==0.2.14
      - widgetsnbextension==4.0.15
      - wrapt==2.0.1
      - xyzservices==2025.10.0
      - yarl==1.22.0
      - zarr==2.18.3
      - zict==3.0.0
      - zipp==3.23.0
prefix: /home/haast026/miniconda3/envs/mosna-survival

or, if you prefer, you can download the Conda environment file here:

• mosna.yml