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Open source projects for proteomics supported by Tokyo Metropolitan Institute of Gerontology


Mass repository for workgroup -- Private mass repository for proteome research work group
We started developing our original repository system for mass spectrometry (MS) data in 2012 as an open source software system. The repository system has been developed as a PostgreSQL-PHP-Apache system for supporting web interfaces. The Micromassrepo (current version: 0.95check This software is licensed under GNU Lesser General Public License. 


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LIPAGE -- Laboratory information management system for 2DPAGE-based proteomics workflow

Most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. The LIPAGE (current version: 0.92check) is a laboratory information management system for 2DPAGE-based proteomics. This is Apache-PHP-PostgreSQL system. Working on alomost any Linux. The project is managed by staffs of the bioinformatics group in Tokyo metropolitan Intitute of gerontology. The LIPAGE is licensed under GNU Lesser General Public License. 
Hiraku Morisawa, Mikako Hirota and Tosifusa Toda: Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow BMC Bioinformatics 2006, 7:430 (04 Oct 2006)

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LIMS Client for 2-D Gel Proteomics

Beta version (0.61) check is released. This version supported data conversion for the XML files exported from the PDQuest system [Bio-Rad laboratories Inc]. Client of LIPAGE (current version: 0.61) is a client software application of our LIMS. It is a data conversion software for the XML files exported from the PDQuest system by Bio-Rad laboratories Inc. It supports to upload 2DPAGE information to LIPAGE. We create a new software application from scratch. Working on only Microsoft Windows 2000 and XP.


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TMIG MASS Data Viewer

Beta version (0.80) check is released. This version supported mzXML and mzML format. They are outputed data from Shimadzu AXIMA TOF2 and sample data in HUPO PSI homepages and The Seattle Proteome Center's homepages. mzXML and mzML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data. TMIG MASS Data Viewer (current version: 0.80) is a tool for the standard file format in Proteomics and an Internet Explorer plugin software in our LIMS, LIPAGE. It is able to open the mzXML and mzML format file . We create a new viewer application from scratch. The combination of the TMIG MASS Data Viewer and the LIPAGE system allows users of LIMS for Proteomics to access accumulated information about mass spectrometric data. TMIG MASS Data Viewer was distributed under the GNU General Public License, which means that its source code is freely distributable and available to the general public. Working on only Microsoft Windows Vista.

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TMIG mzXML Viewer

Beta version (0.80) check is released. This version supported only mzXML data of Shimadzu AXIMA TOF2. mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data. TMIG mzXML Viewer (current version: 0.80) is a tool for the standard file format in Proteomics and an Internet Explorer plugin software in our LIMS, LIPAGE. It is able to open the mzXML format file . We create a new viewer application from scratch. The combination of the TMIG mzXML Viewer and the LIPAGE system allows users of LIMS for Proteomics to access accumulated information about mass spectrometric data. TMIG mzXML Viewer was distributed under the GNU General Public License, which means that its source code is freely distributable and available to the general public. Working on only Microsoft Windows 2000 and XP.

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