---
name: jupyter-notebook-development-python
description: Use when when building reproducible Python-based computational workflows that must serve both beginner and expert users; when the analysis requires interactive parameter tuning, file upload capability, or real-time result visualization;
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3927
  edam_topics:
  - http://edamontology.org/topic_0091
  - http://edamontology.org/topic_3520
  tools:
  - Python
  - Jupyter Lab
  - Sklearn (scikit-learn)
  - Google Colaboratory
  - Tk (Tkinter)
  - Anaconda
  techniques:
  - ion-mobility-MS
derived_from:
- doi: 10.1021/acs.analchem.2c03491
  title: CCS Predictor 2.0
- doi: 10.1101/2022.08.09.503345
  title: ''
evidence_spans:
- CCSP 2.0 is written in Python
- CCSP 2.0 is written in Python and packaged into two notebook forms
- a Jupyter Lab compatible notebook with a Tk interface
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_ccs_predictor_2_0_cq
    doi: 10.1021/acs.analchem.2c03491
    title: CCS Predictor 2.0
  dedup_kept_from: coll_ccs_predictor_2_0_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1021/acs.analchem.2c03491
  all_source_dois:
  - 10.1021/acs.analchem.2c03491
  - 10.1101/2022.08.09.503345
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# Jupyter Notebook Development in Python

## Summary

Develop and deploy Python-based Jupyter notebooks as interactive computational tools for scientific analysis, packaged in multiple execution environments (cloud-hosted and local) to accommodate different user expertise levels and data scales. This skill encompasses notebook architecture, dependency management, graphical interface integration, and deployment across Google Colaboratory and Jupyter Lab platforms.

## When to use

When building reproducible Python-based computational workflows that must serve both beginner and expert users; when the analysis requires interactive parameter tuning, file upload capability, or real-time result visualization; when you need to support both small-scale cloud execution (< 10,000 molecules or records) and large-scale local execution with user-provided training or target datasets.

## When NOT to use

- When your users have no Python experience and cannot tolerate local environment setup; use Google Colab exclusively in this case rather than a dual-variant strategy.
- When prediction requires continuous operation beyond 12 hours; Colaboratory sessions disconnect after this limit, making it unsuitable for batch processing of very large datasets.
- When the analysis does not involve user-curated training sets or interactive parameter selection; a static pipeline or batch script may be more efficient than a notebook interface.

## Inputs

- Python 3 environment (local or cloud-hosted)
- User-curated training dataset (e.g., metabolomics data with known collision cross sections)
- Target dataset for prediction (e.g., unknown metabolomics compounds)
- Model parameters and feature set selections (via UI or notebook cells)
- Requirements.txt or equivalent dependency specification

## Outputs

- Interactive Jupyter notebook (.ipynb) in Google Colab format
- Interactive Jupyter notebook (.ipynb) in Jupyter Lab format with Tk interface
- Filtered prediction results with false positive annotations
- Model performance metrics or validation outputs
- Exportable result files (CSV or equivalent) for downstream analysis

## How to apply

Design two notebook variants: (1) a Google Colaboratory version that requires no local installation, suitable for exploratory work with inherent 12-hour session limits and ~20-minute idle disconnection; (2) a Jupyter Lab version with Tk graphical interface components for users familiar with Python who plan to process large datasets locally. For the local variant, declare all package dependencies (e.g., Sklearn ≥ v1.0.2) in a requirements.txt file and integrate Tk widgets to allow users to upload training data, configure model parameters, and select input feature sets. Embed step-by-step instructions within each notebook variant to guide execution. Validate notebook execution by running cells sequentially and comparing model outputs against reference datasets or ground truth metrics to ensure reproducibility and correctness.

## Related tools

- **Python** (Programming language and execution environment for the notebook kernel)
- **Sklearn (scikit-learn)** (Machine learning library for collision cross section prediction model implementation; requires v1.0.2 or later)
- **Jupyter Lab** (Local notebook editor and execution environment for the Tk-integrated variant intended for large-scale local analysis) — https://jupyter.org/
- **Google Colaboratory** (Cloud-hosted notebook execution platform for the beginner-friendly variant; no local installation required) — https://colab.research.google.com/
- **Tk (Tkinter)** (Graphical user interface library for file upload, parameter configuration, and feature set selection in the local Jupyter Lab variant)
- **Anaconda** (Recommended Python distribution for installing Python 3 and dependency management on local systems) — https://www.anaconda.com/products/distribution

## Evaluation signals

- Notebook executes all cells without errors in both Google Colab and Jupyter Lab environments; no import failures or missing dependencies.
- Model predictions on reference/ground-truth datasets match or closely reproduce the expected outputs documented in the article or repository.
- Tk interface widgets (file upload, parameter controls) respond to user input and pass data correctly to the prediction model in the local variant.
- Google Colab notebook remains responsive and does not disconnect prematurely when run continuously for ≤ 12 hours on typical metabolomics datasets.
- Exported results (filtered predictions with false positive annotations) can be loaded into downstream analysis tools without format corruption or data loss.

## Limitations

- Google Colab enforces a 12-hour continuous operation limit and disconnects after ~20 minutes of inactivity, making it unsuitable for very large batch predictions or integration into long-running analysis pipelines.
- Local Jupyter Lab variant requires Python 3 and manual installation of all dependencies (Sklearn ≥ v1.0.2, Jupyter, Tkinter), creating a higher barrier to entry for non-expert users.
- Tk interface is platform-dependent and may require additional system-level configuration on some operating systems (especially macOS and headless Linux servers).
- Notebook-based approach couples code, documentation, and data, which may hinder version control, code reuse in non-notebook contexts, or integration into larger automated pipelines.

## Evidence

- [readme] CCSP 2.0 is written in Python and packaged into two notebook forms: (1) a Google Colaboratory Jupyter notebook that is well suited for beginners, and (2) a Jupyter Lab compatible notebook with a Tk interface for users more familiar with Python.: "CCSP 2.0 is written in Python and packaged into two notebook forms: (1) a Google Colaboratory Jupyter notebook that is well suited for beginners, and (2) a Jupyter Lab compatible notebook with a Tk"
- [readme] If you plan to use CCSP 2.0 only to make small scale predictions (<10,000 molecules) and export your results to your local computer, the Google Colab option is recommended. This route does not require you to install Python or any of the packages required to run the code, as all calculations are performed through Google hosted services.: "If you plan to use CCSP 2.0 only to make small scale predictions (<10,000 molecules) and export your results to your local computer, the Google Colab option is recommended."
- [readme] Google Colab will only allow continuous notebook operation for up to 12 hours and will disconnect after ~20 minutes if left idle.: "Google Colab will only allow continuous notebook operation for up to 12 hours and will disconnect after ~20 minutes if left idle."
- [readme] If you plan to predict CCS values using large training or target sets or if you plan to integrate the code into a larger analysis workflow, the locally hosted Jupyter Lab version is recommended.: "If you plan to predict CCS values using large training or target sets or if you plan to integrate the code into a larger analysis workflow, the locally hosted Jupyter Lab version is recommended."
- [readme] The current version of CCSP 2.0 requires Sklearn V1.0.2 or later. A full list of package requirements is available in the requirements.txt file.: "The current version of CCSP 2.0 requires Sklearn V1.0.2 or later. A full list of package requirements is available in the requirements.txt file."
- [other] Integrate the Tk graphical interface components to allow users to upload training data, configure model parameters, and select input feature sets.: "Integrate the Tk graphical interface components to allow users to upload training data, configure model parameters, and select input feature sets."
- [readme] Follow the instructions embedded within the notebook.: "Follow the instructions embedded within the notebook."