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PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface.
A collection of cheminformatics and machine-learning software written in C++ and Python.
NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit
The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java.
Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
A pipeline for quantitative proteomics based upon isobaric tags
...IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn.
The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".
MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
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