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The metabolomics standards initiative (msi) will develop a Core Information for Metabolomics Reporting (CIMR) recommendation and a more formal and semantically defined corresponding ontology (msi-ontology).
PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format
LaboLIM is a laboratory information system aimed at microbiology laboratories. It is licensed under the GPL V3.0. It is written in PHP and currently uses SQLite 2.1, but could be converted to MySQL.
It was partially developed with a working micro lab.
Looking for some people to chip in and make it a nice project.