Quantum software platform that is optimized across the quantum stack
This repository is the home of the Superstaq development team's open-source work. Our quantum software platform is optimized across the quantum stack and enables users to write quantum programs in Cirq or Qiskit and target a variety of quantum computers and simulators.
Find active modules in metabolic networks using high-throughput data
...If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest!
AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulatedannealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism.
For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. ...
Open Metaheuristic (oMetah) is a library aimed at the conception and the rigourous testing of metaheuristics (i.e. genetic algorithms, simulatedannealing, ...). The code design is separated in components : algorithms, problems and a test report generator