The Comprehensive Systems Biology Project (CSB)
- A Comprehensive Systems-Biology Database -
Hosted at Max Planck Institute of Molecular Plant Physiology
Databases: Associated DB | Transcriptome DB | Metabolome DB | Co-Response DB | BestFit
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NOTIFICATION: Permanent migration of all CSB.DB services and functionalities on 1.1.2016.
Herewith we inform you that all CSB.DB databases have been migrated at the beginning of 2016. This includes all gene correlation and expression databases, the GMD@CSB.DB module and all associated databases
The BestFit software, a tool for non-aqueous fractionation data analysis, will also be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
We thank all users, contributors, and collaborators of CSB.DB at the Max Planck Institute for their long-standing support.
Yours sincerely, the CSB.DB Curator and the CSB.DB Developmental Core Team
CSB.DB Structure
CSB.DB represents the public interface of the Comprehensive Systems-Biology Project (CSB) and is hosted at the Max Planck Institute of Plant Molecular Physiology. This page provides insight into the general and database structure of CSB.DB.

To get information of your choice use the links listed below.
General Structure

CSB.DB: The General Structure get picture back to top

CSB.DB is accessible over the Internet using a web browser and allows for flexible and remote access, without the need for special software on the client computers. Software, information and help files will continually be updated and therefore will be automatically available to all users. CSB.DB can be easily accessed from multiple operating platforms (MacOS, UNIX, Linux, and Windows). The sole requirements being a JavaScript enabled browser, supplied with most modern operating systems, and the ability to display PDF files. CSB.DB runs on a multiprocessor SuSE Linux server under the Apache web server, and uses SAPDB as a database management system that stores the results of the pre-computed statistical calculations. CGI scripts are implemented in the PERL language, in conjunction with the mod_perl module. The PERL/-CGI scripts function as the interf ace to connect the user queries with the database. Beyond this 'classical' structure of a web database the PERL language is also used to interlink and to transfer information to the statistical software package R. Validation as well as extensive statistics, such as bootstrap and jackknife analyses, are implemented as R scripts which can be invoked upon user selection. Beyond it graphical visualisation is done with R which produces PDF files that are automatically displayed and can be saved for further reference.
Database Structure

CSB.DB: The Database Structure get picture back to top

In the current version of CSB.DB the public databases are subdivided into three major parts. The first part covers the statistical analyses applied to expression profile data which were generated on different microarray technology platforms. This part, called 'Co-Response Databases' currently contains the gene-gene correlations of the prokaryotic model organism Escherichia coli (EcoCoR@CS.DB), the eukaryotic model organism Saccharomyces cerevisiae (SceCoR@CSBDB) and the eukaryotic plant model organism Arabidopsis thaliana (AthCoR@CSB.DB). Pair wise gene correlations can be obtained e.g. via the 'Single Gene Query Page (sGQ)', which allows the user to insert a gene of interest and get all significantly positive or negative associated genes. The statistic parameters, which mean the probability, the confidence interval and the power of the applied test, are dynamically calculated based on the underlying test distribution of the respective correlation coefficient. Moreover a detailed statistical analysis can be obtained for a selected gene pair by user validation of output. Beyond it, the validation allows the detection of outliers, which may be associated with technical errors, biological variance or can represent a biological regulatory event, as well as a variety of graphical plots. The second part will focus on analytical techniques whereas the third part covers CSB.DB Associated Web Pages, like the Plant Subtilase Database (PSDB), which were featured and maintained by CSB.DB Development Core Team. The associated web pages contain predominantly manually curated gene annotations of specialists having specific research interests and beyond that they provide experimentally derived results.

For suggestions and questions feel free to contact the CSB.DB curator.
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