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MassChroQ

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MassChroQ (Mass Chromatogram Quantification) software performs quantification of data obtained from mass-spectrometry techniques. It is particularly well suited for peptide quantification of LC-MS (Liquid Chromatography - Mass Spectrometry) data. It performs chromatographic alignment, XIC extraction, peak detection and quantification on identified peptides, with or without isotopic labeling, on high or low resolution data and it takes into account peptide or protein fractionation.

Bioconductor

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Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

The Bioconductor release version is updated twice each year, and is appropriate for most users. There is also a development version, to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations.

IDRT - Integrated Data Repository Toolkit

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i2b2 has turned out to be a very valuable component for secondary use of routine clinical data. Its pragmatic database schema allows merging of data from heterogeneous data sources, and the intuitive user interface enables easy querying and powerful processing. However, it's a component rather than a complete solution: The user is facing several barriers when integrating i2b2 into the operational workflow.

OBiBa

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OBiBa software consists of a suite of stand-alone applications that support various study's data management activities. These modular applications can be integrated to create a comprehensive information management and analysis system for individual studies.

As part of the Maelstrom Research program, OBiBa suite includes advanced software components enabling data harmonization and federation for study networks that aim to harmonize and share securely data among their members.

MOLGENIS

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MOLGENIS is a modular web application for scientific data. MOLGENIS was born from molecular genetics research (and was called 'molecular genetics information system') but has grown, thanks too many sponsors and contributors, to be used in many scientifc areas such as biobanking, rare disease research, patient registries and even energy research. MOLGENIS provides researchers with user friendly and scalable software infrastructures to capture, exchange, and exploit the large amounts of data that is being produced by scientific organisations all around the world.

i2b2

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i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origins. This platform currently enjoys wide international adoption by the CTSA network, academic health centers, and industry.