Bioinformatics
Bioinformatics Learning Resources
Bioinformatics is a field of computational science that has to do with the analysis of sequences of biological molecules. This usually refers to genes, DNA, RNA, or protein, and is particularly useful in comparing genes and other sequences in proteins and other sequences within an organism or between organisms, looking at evolutionary relationships between organisms, and using the patterns that exist across DNA and protein sequences to figure out what their function is.
European Bioinformatics Institute
National Center for Biotechnology Information
Online Courses in Bioinformatics |ISCB - International Society for Computational Biology
Top Bioinformatics Courses | Udemy
Learn Bioinformatics with Online Courses and Lessons | edX
Bioinformatics Graduate Certificate | Harvard Extension School
Bioinformatics and Biostatistics | UC San Diego Extension
Bioinformatics and Proteomics - Free Online Course Materials | MIT
Introduction to Biometrics course - Biometrics Institute
Bioinformatics Tools, Libraries, and Frameworks
Bioconductor is an open source project that provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and Docker images.
Bioconda is a channel for the conda package manager specializing in bioinformatics software. It has a repository of packages containing over 7000 bioinformatics packages ready to use with conda install.
UniProt is a freely accessible database that provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (mammalian) genomes.
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
BioRuby is a toolkit that has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.
BioJava is a toolkit that provides an API to maintain local installations of the PDB, load and manipulate structures, perform standard analysis such as sequence and structure alignments and visualize them in 3D.
BioPHP is an open source project that provides a collection of open source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools.
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
Ascalaph Designer is a program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs.
Anduril is a workflow platform for analyzing large data sets. Anduril provides facilities for analyzing high-thoughput data in biomedical research, and the platform is fully extensible by third parties. Ready-made tools support data visualization, DNA/RNA/ChIP-sequencing, DNA/RNA microarrays, cytometry and image analysis.
Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis.
PathVisio is a free open-source pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. It is developed in Java and can be extended with plugins.
Orange is a powerful data mining and machine learning toolkit that performs data analysis and visualization.
Basic Local Alignment Search Tool is a tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
OSIRIS is public-domain, free, and open source STR analysis software designed for clinical, forensic, and research use, and has been validated for use as an expert system for single-source samples.
NCBI BioSystems is a Database that provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez.