Getting Started#
To get started simply follow the sections tutorials in this Jupyter Book or find the code online at our GitHub.
Attending ISMB ‘24 Tutorial IP5: Modelling Multi-Modal Biomedical Data Using Networks#
For those of you attending our tutorial at ISMB ‘24 we have a dedicated Jupyter server with all data and code already available here. Simply use your dedicated username and password.
External Users#
These notebooks and code are designed for the ISMB 2024 tutorial in Montreal, however, we encourage those interested in multi modal data modelling using networks to interact with the code, notebooks and the team.
All code required to execute this tutorial are provided as part of this book. All data is placed on the University of Edinburgh DataShare resource with a permanent DOI so it is available in perpetuity. Please contact a member of the team if you have any questions.
All materials require a working installation of Python with the package requirements shown below.
Requirements#
Package Version
------------------------ ------------------
annotated-types 0.7.0
astropy 6.1.0
astropy-iers-data 0.2024.6.3.0.31.14
asttokens 2.0.5
beautifulsoup4 4.12.2
biothings-client 0.2.6
Bottleneck 1.3.7
Brotli 1.0.9
certifi 2024.6.2
charset-normalizer 2.0.4
comm 0.2.1
contourpy 1.2.0
cycler 0.11.0
debugpy 1.6.7
decorator 5.1.1
dgl 2.1.0
exceptiongroup 1.2.0
executing 0.8.3
filelock 3.14.0
fonttools 4.51.0
fsspec 2024.6.0
gseapy 1.1.3
html5lib 1.1
idna 3.7
ipykernel 6.28.0
ipython 8.20.0
jedi 0.18.1
Jinja2 3.1.4
joblib 1.4.0
jsonpickle 3.2.1
jupyter_client 8.6.0
jupyter_core 5.5.0
kiwisolver 1.4.4
lxml 5.2.1
MarkupSafe 2.1.5
matplotlib 3.8.4
matplotlib-inline 0.1.6
mkl-fft 1.3.8
mkl-random 1.2.4
mkl-service 2.4.0
mpmath 1.3.0
mygene 3.2.2
nest-asyncio 1.6.0
networkx 3.2.1
numexpr 2.8.7
numpy 1.26.4
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 8.9.2.26
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.5.40
nvidia-nvtx-cu12 12.1.105
packaging 23.2
palettable 3.3.3
pandas 2.2.1
parso 0.8.3
pexpect 4.8.0
pillow 10.3.0
pip 24.0
platformdirs 3.10.0
plotly 5.19.0
ply 3.11
prettytable 3.10.0
prompt-toolkit 3.0.43
psutil 5.9.0
ptyprocess 0.7.0
pure-eval 0.2.2
pydantic 2.7.3
pydantic_core 2.18.4
pyerfa 2.0.1.4
Pygments 2.15.1
pyparsing 3.0.9
PyQt5 5.15.10
PyQt5-sip 12.13.0
PySocks 1.7.1
python-dateutil 2.9.0.post0
pytz 2024.1
pyvis 0.3.2
PyYAML 6.0.1
pyzmq 25.1.2
requests 2.32.2
scikit-learn 1.4.2
scipy 1.13.1
seaborn 0.13.2
setuptools 69.5.1
sip 6.7.12
six 1.16.0
snfpy 0.2.2
soupsieve 2.5
stack-data 0.2.0
sympy 1.12.1
tenacity 8.2.2
threadpoolctl 2.2.0
tomli 2.0.1
torch 2.3.1
torchdata 0.7.1
tornado 6.3.3
tqdm 4.66.4
traitlets 5.7.1
triton 2.3.1
typing_extensions 4.12.2
tzdata 2023.3
unicodedata2 15.1.0
urllib3 2.2.1
wcwidth 0.2.5
webencodings 0.5.1
wheel 0.43.0