Containing the Deluge
19/03/12 14:59 Filed in: GenomeWeb Daily Scan
Submitted by S. Pelech - Kinexus on Mon, 03/19/2012 - 14:58.
At Kinexus Bioinformatics Corporation, we originally had custom algorithms produced from a local software company to manage the data that was being generated with our custom multi-immunoblotting analyses. This handled nearly a million measurements of the expression and phosphorylation of proteins, and some of this is still currently available for open-access at the KiNET website (www.kinet.ca). Unfortunately, about 4 years ago the firm went out of business and since then we have been unable to update or modify their proprietary software. This is a major risk for any life science company that relies on customized software from a specialized software developer.
We have found that MS-Access and MS-SQL databases serve best for storage of proteomics data and in the last few years we have now focused on using off the shelf programming software to create web-based interfaces that permit users to access this data. This has allowed us to produce our PhosphoNET (www.phosphonet.ca) and TranscriptoNET (www.transcriptonet.ca) KnowledgeBases with open-access information on human protein phosphorylation and mRNA expression data. For initial collection and annotation of data, we use MS-Excel due to its relative ease of use and versatility, and then we later import the data into the MS-Access and MS-SQL databases. In the design of our upcoming web-based data- and knowledge-bases, we are attempting to facilitate their seamless integration with each other and other major public and private repositories of information on genes and proteins. In this way, users can retrieve a wide range of comprehensive data with minimal steps.
Link to the original blog post.
At Kinexus Bioinformatics Corporation, we originally had custom algorithms produced from a local software company to manage the data that was being generated with our custom multi-immunoblotting analyses. This handled nearly a million measurements of the expression and phosphorylation of proteins, and some of this is still currently available for open-access at the KiNET website (www.kinet.ca). Unfortunately, about 4 years ago the firm went out of business and since then we have been unable to update or modify their proprietary software. This is a major risk for any life science company that relies on customized software from a specialized software developer.
We have found that MS-Access and MS-SQL databases serve best for storage of proteomics data and in the last few years we have now focused on using off the shelf programming software to create web-based interfaces that permit users to access this data. This has allowed us to produce our PhosphoNET (www.phosphonet.ca) and TranscriptoNET (www.transcriptonet.ca) KnowledgeBases with open-access information on human protein phosphorylation and mRNA expression data. For initial collection and annotation of data, we use MS-Excel due to its relative ease of use and versatility, and then we later import the data into the MS-Access and MS-SQL databases. In the design of our upcoming web-based data- and knowledge-bases, we are attempting to facilitate their seamless integration with each other and other major public and private repositories of information on genes and proteins. In this way, users can retrieve a wide range of comprehensive data with minimal steps.
Link to the original blog post.