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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
Chemical structures database & machine learning with web services API
AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials.
Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases.
Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
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The development and curation of a range of XML-based tools
for using Chemical Markup Language (CML), including
XSD XML Schemas for validation, datatyping and constraining CML
documents and XSLT Stylesheets for transforming, filtering and rendering.
primeHandle is a set of data management tools in support of the PrIMe Initiative (http://primekinetics.org). primeHandle includes graphical user interfaces for searching through data collections, editing and submitting data to the PrIMe Data Depository.
Goldify is a set of tools that allow automated addition of links into electronic documents. Its main purpose is to allow such addition of links into documents that wish to link to the IUPAC GoldBook (http://goldbook.iupac.org).
The aim of the project is to provide open source collection of algorithms in the field of spectroscopy: data handling and processing, modeling and artificial intelligence tools.
The CheckCML project is a collection of modules for the production and checking of chemical experimental data represented as CML. The core CheckCML library provides classes for the checking process; tools such as OscarData allow for the production of CML
JTabler is for the simple table manager to utilize other programs, including many internet utilities, statistics tools, especially adapted for chemistry data such as SDF and MOL
Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.
OpenChem Workbench is an enterprise software suite designed for creating, saving, searching, and exchanging chemical data. It uses existing tools (NIST, Gaussian, CHEMKIN) and its own (easy molecule building, mechanism management, group additivity, etc.)
The JPAT API is a Java API designed to provide developers with tools for calculating the results of protease digestion of proteins and ms/ms fragmentation of peptides. JPAT also contains GUI components for displaying the results. JPAT is a nice way to get