Computational biomedicine resources

Tutorials

• sandbox.bio Bioinformatics tutorials with an in-browser interactive Terminal.
• ROSALIND Gamified tutorials in Python and bioinformatics.
• RDKit cookbook Code recipes for molecule handling, descriptor calculation, substructure searching, fingerprints.
• Practical Cheminformatics Jupyter notebooks covering a variety of cheminformatics tasks.

Blogs

Bioinformatics

• EMBL-EBI Train Online Case studies from EBI.

Cheminformatics

• RDKit Blog Walkthroughs of tasks in RDKit (Python cheminformatics toolkit).
• Pat Walters Strong opinions on cheminformatics, often with code.
• iwatobipen Snippets of code for particular problems.

Open source software / packages

Bioinformatics

• Galaxy Webserver for running a range of common bioinformatics tasks.
• Biopython Python tools for sequence analysis, structural bioinformatics.
• scikit-bio Statistical analysis and visualization for biological data in Python.
• SAMtools Reading, writing, and processing of high-throughput sequencing data.
• BWA & Bowtie2 Aligners for mapping sequencing reads.
• Nextflow Workflow engine for scalable, reproducible pipelines.
• Cytoscape Network visualization for gene/protein interaction data.

Databases & Repositories

Bioinformatics

• NCBI GenBank, SRA, GEO.
• UniProt Protein sequences & annotations.

Cheminformatics

• PubChem
• ChEMBL
• ZINC Ready-to-dock, commercially available compounds.
• Protein Data Bank (PDB) Structures of biomolecules.

Communities & Forums

• BioStars Q&A for bioinformatics.
• SEQanswers Sequencing community.