Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow
| Autor: | Tosifusa Toda, Mikako Hirota, Hiraku Morisawa |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2006 |
| Předmět: |
Proteomics
Proteomics methods Computer science Interface (computing) 2 d gels Information Storage and Retrieval Mass spectrometry lcsh:Computer applications to medicine. Medical informatics Biochemistry Peptide Mapping Field (computer science) User-Computer Interface Structural Biology Computer Graphics Electrophoresis Gel Two-Dimensional Databases Protein Molecular Biology lcsh:QH301-705.5 Gel electrophoresis Flexibility (engineering) Internet Information Dissemination Applied Mathematics Computational Biology Data science Computer Science Applications Management information systems Electrophoresis Workflow lcsh:Biology (General) Proteome Database Management Systems lcsh:R858-859.7 DNA microarray Laboratories Software |
| Zdroj: | BMC Bioinformatics, Vol 7, Iss 1, p 430 (2006) BMC Bioinformatics |
| ISSN: | 1471-2105 |
| Popis: | Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved. |
| Databáze: | OpenAIRE |
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