Table Icon Open Databases
Name & Short Story Link
brain-map.org: Allen Institute for Brain Science provides RNA-Seq datasets. Citing is a must.
andrewjanowczyk.com: Deep learning for digital pathology image analysis.
broadinstitute.org: Broad Bioimage Benchmark Collection (BBBC): A collection of freely downloadable microscopy image sets, cited in 500+ studies.
cellimagelibrary.org: Bioimage database of the University of California, San Diego
expasy.org: Swiss Bioinformatics Resource Portal referencing to all kinds of different biological subjects.
gapminder.org: Gapminder is an independent educational non-profit fighting global misconceptions. Selected data categories: Energy, Environment, Health, Infrastructure and Employment
datasetsearch.research.google.com: Google search engine for datasets
kaggle.com: Machine Learning and Data Science Community database
ncbi.nlm.nih.gov: "The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information."
openmicroscopy.org: Image Data Resource (IDR): Public repository of high-quality bio-image datasets from scientific studies.
ourworldindata.org: "Research and data to make progress against the world's largest problem". Database providing datasets to Population and Demographic Change, Health, Energy and Environment, Food and Agriculture, Education and Knowledge, Innovation and Technological Change and much more.
Table Icon Literature
Title Author Tags
Mastering Python for Bioinformatics: How to Write Flexible, Documented, Tested Python Code for Research Computing Ken Youens-Clark
Python for Biologists: A complete programming course for beginners
Advanced Python for Biologists
Effective Python Development for Biologists: Tools and techniques for building biological programs 		Martin Jones
Deep Learning for the Life Sciences: Applying Deep Learning to Genomics, Microscopy, Drug Discovery, and More Bharath Ramsundar
et al.
Python Programming for Biology (Bioinformatics and Beyond) Tim J. Stevens
et al.
Table Icon Online Lectures and Workshops
Name & Short Story Link
Youtube: A. Foucart's Introduction to bioimage processing (GITHUB REPOSITORY)
Github: A. Foucart's Introduction to bioimage processing
rosalind.info: Rosalind is a platform for learning bioinformatics and programming through problem solving
Youtube: Sreenivas B's Python tutorials for image processing and machine learning
Github: Sreenivas B's Python tutorials for image processing and machine learning (GITHUB REPOSITORY)
Table Icon py modules
Name & Short Story Link
biopython.org: "Biopython is a set of freely available tools for biological computation written in Python by an international team of developers."
opencv.org: "OpenCV (Open Source Computer Vision Library: http://opencv.org) is an open-source library that includes several hundreds of computer vision algorithms."
deepchem.io: "DeepChem is a Python library for machine learning and deep learning on molecular and quantum datasets. It is built on top of PyTorch, and other popular ML frameworks. It is designed to make it easy to apply ML to new domains, and to build and benchmark new models. It is also designed to make it easy to use ML in production, by providing easy-to-use model export and deployment APIs."
python-pillow.org: "The Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, an efficient internal representation, and fairly powerful image processing capabilities. The core image library is designed for fast access to data stored in a few basic pixel formats. It should provide a solid foundation for a general image processing tool."
scipy.org: "SciPy provides algorithms for optimization, integration, interpolation, eigenvalue problems, algebraic equations, differential equations, statistics and many other classes of problems."
scikit-image.org: "scikit-image is a collection of algorithms for image processing."