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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.
A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace: Centralized web application that provides data format transformations and facilitates connections with other bioinformatics ...
A agent-based [20] modeling framework for multicellular systems biology. multiplatform (C++) BSD-3: Yes, but only for reactions PySCeS: 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 ...
Galaxy [2] is an open-source scientific workflow system designed to make research accessible, reproducible, and transparent. Originally developed for computational biology, Galaxy has evolved into a domain-agnostic framework utilized across various scientific disciplines.
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.
Most data visualization in systems biology is done using mathematically generated models. Researchers will diagram all of the protein, gene, or metabolic pathways in a given biological system, then determine the speed of the reactions in that system using mass action kinetics or enzyme kinetics.
pathway based data integration and visualization, easy to use and integrate into pathway analysis multiplatform (R/Bioconductor) GPL: SBMLDiagrams [2] Python API to display and edit SBML layout/render extension: multiplatform: MIT: Systrip: analysis of time-series data in the context of biological networks Windows, Linux: LGPL, GPL
Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern comparative analyses or population genetics, while others do non-phylogenetic multivariate analysis.