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The Biopython project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers. [ 1 ] [ 4 ] [ 5 ] It contains classes to represent biological sequences and sequence annotations , and it is able to read and write to a variety of file formats.
Open Bioinformatics Foundation: Biopython: Python language toolkit Cross-platform: Biopython [2] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit Linux, macOS, Windows [3] GPL v2 or Ruby: Open Bioinformatics Foundation: BLAST: Algorithm and program for comparing primary biological sequence information, including DNA and protein ...
Python tool for modeling and analyzing SBML models [21] [22] [23] multiplatform (Python) BSD-3: Yes pySB: Python-based [24] platform with specialization in rule-based models. multiplatform (Python) BSD-3: Partial ReaDDy: Particle-based spatial simulator with intermolecular potentials [25] Linux and Mac: Custom: Not applicable SBSCL
The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling. [1]The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations.
Computational biology is a specialized domain that often requires knowledge of computer programming. Galaxy aims to give biomedical researchers access to computational biology without also requiring them to understand computer programming. [13] [14] Galaxy does this by stressing a simple user interface [15] over the ability to build complex ...
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
Biskit is an open source software package that facilitates research in structural bioinformatics and molecular modelling.Written in Python, it consists of: . An object-oriented programming library for manipulating and analyzing macromolecular structures, protein complexes and molecular dynamics trajectories
Rosalind is an educational resource and web project for learning bioinformatics through problem solving and computer programming. [1] [2] [3] Rosalind users learn bioinformatics concepts through a problem tree that builds up biological, algorithmic, and programming knowledge concurrently or learn by topics, with the topic of Alignment, Combinatorics, Computational Mass Spectrometry, Heredity ...