Notebooks
Compute environment
Features
Notebooks
Compute environment
Mantle Notebooks run in the cloud, so you don’t have to worry about occupying your computer’s resources (like storage, RAM, CPUs or GPUs) or installing any software on your own computer. This guide provides information on the hardware and preinstalled packages that come with every notebook, as well as instructions for customizing your environment.
Hardware
| Compute | 2 CPU |
| Memory | 4 GB |
| GPU | Available on request |
| Storage | 10 GB |
| Internet access | Yes |
Please contact us if this configuration does not suit your needs.
Preconfigured packages
To help you get started fast, all Mantle Notebooks come with the following kernels:
Default kernel
For general purpose biological data analysis
- Python 3.12
Package Version
----------------------------- ------------
alembic 1.12.0
anyio 4.0.0
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
arrow 1.3.0
asttokens 2.4.0
async-generator 1.10
async-lru 2.0.4
attrs 23.1.0
Babel 2.13.0
backcall 0.2.0
backports.functools-lru-cache 1.6.5
beautifulsoup4 4.12.2
bleach 6.1.0
blinker 1.6.3
boltons 23.0.0
boto3 1.35.59
botocore 1.35.59
Brotli 1.1.0
cached-property 1.5.2
cachetools 5.5.0
certifi 2023.7.22
certipy 0.1.3
cffi 1.16.0
charset-normalizer 3.3.0
colorama 0.4.6
comm 0.1.4
conda 23.9.0
conda-package-handling 2.2.0
conda_package_streaming 0.9.0
cryptography 41.0.4
debugpy 1.8.0
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
exceptiongroup 1.1.3
executing 1.2.0
fastjsonschema 2.18.1
fqdn 1.5.1
google-auth 2.36.0
greenlet 3.0.0
idna 3.4
importlib-metadata 6.8.0
importlib-resources 6.1.0
ipykernel 6.25.2
ipython 8.16.1
ipython-genutils 0.2.0
isoduration 20.11.0
jedi 0.19.1
Jinja2 3.1.2
jmespath 1.0.1
json5 0.9.14
jsonpatch 1.33
jsonpointer 2.4
jsonschema 4.19.1
jsonschema-specifications 2023.7.1
jupyter_client 8.4.0
jupyter_core 5.4.0
jupyter-events 0.8.0
jupyter-lsp 2.2.0
jupyter_server 2.8.0
jupyter_server_terminals 0.4.4
jupyter-telemetry 0.1.0
jupyterhub 4.0.2
jupyterlab 4.0.7
jupyterlab-pygments 0.2.2
jupyterlab_server 2.25.0
libmambapy 1.5.2
Mako 1.2.4
mamba 1.5.2
mantlebio 2.1.1
mantlelab 0.1
MarkupSafe 2.1.3
matplotlib-inline 0.1.6
mistune 3.0.1
nbclassic 1.0.0
nbclient 0.8.0
nbconvert 7.9.2
nbformat 5.9.2
nest-asyncio 1.5.8
notebook 7.0.6
notebook_shim 0.2.3
numpy 1.26.4
oauthlib 3.2.2
overrides 7.4.0
packaging 23.2
pamela 1.1.0
pandas 2.2.3
pandocfilters 1.5.0
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pip 23.3
pkgutil_resolve_name 1.3.10
platformdirs 3.11.0
pluggy 1.3.0
prometheus-client 0.17.1
prompt-toolkit 3.0.39
protobuf 5.28.3
psutil 5.9.5
ptyprocess 0.7.0
pure-eval 0.2.2
pyasn1 0.6.1
pyasn1_modules 0.4.1
pycosat 0.6.6
pycparser 2.21
pycurl 7.45.1
Pygments 2.16.1
PyJWT 2.8.0
pyOpenSSL 23.2.0
PySocks 1.7.1
python-dateutil 2.8.2
python-dotenv 1.0.1
python-json-logger 2.0.7
pytz 2023.3.post1
PyYAML 6.0.1
pyzmq 25.1.1
referencing 0.30.2
requests 2.31.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.10.6
rsa 4.9
ruamel.yaml 0.17.39
ruamel.yaml.clib 0.2.7
s3transfer 0.10.3
Send2Trash 1.8.2
setuptools 68.2.2
six 1.16.0
sniffio 1.3.0
soupsieve 2.5
SQLAlchemy 2.0.22
stack-data 0.6.2
terminado 0.17.1
tinycss2 1.2.1
tomli 2.0.1
tornado 6.3.3
tqdm 4.66.1
traitlets 5.11.2
truststore 0.8.0
types-python-dateutil 2.8.19.14
typing_extensions 4.8.0
typing-utils 0.1.0
tzdata 2024.2
uri-template 1.3.0
urllib3 2.0.7
wcwidth 0.2.8
webcolors 1.13
webencodings 0.5.1
websocket-client 1.6.4
wheel 0.41.2
zipp 3.17.0
zstandard 0.21.0
cytoflow kernel
For analysis of flow cytometry data using the cytoflow package
- Python 3.11.6
Package Version
----------------------------- ------------
alembic 1.12.0
anyio 4.0.0
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
arrow 1.3.0
asttokens 2.4.0
async-generator 1.10
async-lru 2.0.4
attrs 23.1.0
Babel 2.13.0
backcall 0.2.0
backports.functools-lru-cache 1.6.5
beautifulsoup4 4.12.2
bleach 6.1.0
blinker 1.6.3
boltons 23.0.0
boto3 1.35.53
botocore 1.35.53
Brotli 1.1.0
cached-property 1.5.2
cachetools 5.5.0
certifi 2023.7.22
certipy 0.1.3
cffi 1.16.0
charset-normalizer 3.3.0
colorama 0.4.6
comm 0.1.4
conda 23.9.0
conda-package-handling 2.2.0
conda_package_streaming 0.9.0
cryptography 41.0.4
debugpy 1.8.0
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
exceptiongroup 1.1.3
executing 1.2.0
fastjsonschema 2.18.1
fqdn 1.5.1
google-auth 2.35.0
greenlet 3.0.0
idna 3.4
importlib-metadata 6.8.0
importlib-resources 6.1.0
ipykernel 6.25.2
ipython 8.16.1
ipython-genutils 0.2.0
isoduration 20.11.0
jedi 0.19.1
Jinja2 3.1.2
jmespath 1.0.1
json5 0.9.14
jsonpatch 1.33
jsonpointer 2.4
jsonschema 4.19.1
jsonschema-specifications 2023.7.1
jupyter_client 8.4.0
jupyter_core 5.4.0
jupyter-events 0.8.0
jupyter-lsp 2.2.0
jupyter_server 2.8.0
jupyter_server_terminals 0.4.4
jupyter-telemetry 0.1.0
jupyterhub 4.0.2
jupyterlab 4.0.7
jupyterlab-pygments 0.2.2
jupyterlab_server 2.25.0
libmambapy 1.5.2
Mako 1.2.4
mamba 1.5.2
mantlebio 2.1.1
mantlelab 0.1
MarkupSafe 2.1.3
matplotlib-inline 0.1.6
mistune 3.0.1
nbclassic 1.0.0
nbclient 0.8.0
nbconvert 7.9.2
nbformat 5.9.2
nest-asyncio 1.5.8
notebook 7.0.6
notebook_shim 0.2.3
numpy 1.26.4
oauthlib 3.2.2
overrides 7.4.0
packaging 23.2
pamela 1.1.0
pandas 2.2.3
pandocfilters 1.5.0
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pip 23.3
pkgutil_resolve_name 1.3.10
platformdirs 3.11.0
pluggy 1.3.0
prometheus-client 0.17.1
prompt-toolkit 3.0.39
protobuf 5.28.3
psutil 5.9.5
ptyprocess 0.7.0
pure-eval 0.2.2
pyasn1 0.6.1
pyasn1_modules 0.4.1
pycosat 0.6.6
pycparser 2.21
pycurl 7.45.1
Pygments 2.16.1
PyJWT 2.8.0
pyOpenSSL 23.2.0
PySocks 1.7.1
python-dateutil 2.8.2
python-dotenv 1.0.1
python-json-logger 2.0.7
pytz 2023.3.post1
PyYAML 6.0.1
pyzmq 25.1.1
referencing 0.30.2
requests 2.31.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.10.6
rsa 4.9
ruamel.yaml 0.17.39
ruamel.yaml.clib 0.2.7
s3transfer 0.10.3
Send2Trash 1.8.2
setuptools 68.2.2
six 1.16.0
sniffio 1.3.0
soupsieve 2.5
SQLAlchemy 2.0.22
stack-data 0.6.2
terminado 0.17.1
tinycss2 1.2.1
tomli 2.0.1
tornado 6.3.3
tqdm 4.66.1
traitlets 5.11.2
truststore 0.8.0
types-python-dateutil 2.8.19.14
typing_extensions 4.8.0
typing-utils 0.1.0
tzdata 2024.2
uri-template 1.3.0
urllib3 2.0.7
wcwidth 0.2.8
webcolors 1.13
webencodings 0.5.1
websocket-client 1.6.4
wheel 0.41.2
zipp 3.17.0
zstandard 0.21.0
Adding packages
You can install additional packages into your notebook’s environment using pip.
Add a new code cell and run !pip install <package_name>. This will immediately install the package.