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List of free analog and digital electronic circuit simulators, available for Windows, macOS, Linux, and comparing against UC Berkeley SPICE.The following table is split into two groups based on whether it has a graphical visual interface or not.
Gene Designer is a computer software package for bioinformatics. [ 1 ] [ 2 ] It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design, [ 3 ] clone, and validate genetic sequences.
The first natural gene circuit studied in detail was the lac operon.In studies of diauxic growth of E. coli on two-sugar media, Jacques Monod and Francois Jacob discovered that E.coli preferentially consumes the more easily processed glucose before switching to lactose metabolism.
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 ...
Maximum likelihood, stochastic heuristics (genetic algorithm, metapopulation genetic algorithm, simulated annealing, etc.), discrete Gamma rate heterogeneity, ancestral state reconstruction, model testing: Michel C. Milinkovitch and Raphaël Helaers MicrobeTrace: MicrobeTrace is a free, browser-based web application.
COPASI is the result of an international collaboration between the University of Manchester (UK), the University of Heidelberg (Germany), and the Virginia Bioinformatics Institute (USA).
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Gene Set Association Analysis for RNA-Seq GSAASeq are computational methods that assess the differential expression of a pathway/gene set between two biological states based on sequence count data. GeneSCF a real-time based functional enrichment tool with support for multiple organisms.