Project members

• Janneke (owner)
• Kees Van Bochove (owner)
• Robert (owner)
• Taco Steemers (owner)
• Tjeerd (owner)

Welcome to project nugoctdwebapp

Usage

The NuGO Clean Transcriptome Database is a module of the  Nutritional Phenotype database that allows users to submit their transcriptome data in the raw format (*.CEL files). Along the way the data is processed, normalized and stored. Users are asked to provide an experiment title and are allowed to arrange the individual hybridizations into groups of biological repeats for statistical needs.

A global password is provided making the CTD safe for external access. In addition, laboratory protocols can be uploaded, edited and shared. Programmable access is provided by JSON http requests directly  (protocol). JSON examples with a password are found on the  example page

The main advantage of the Clean Transcriptome Database is the equal normalization of CEL files using RMA and GRSN (global rank-invariant set normalization,  pubmed. GRSN ensures samples within a dataset are fitted to an average intensitiy distribution allowing for a more robust comparison. However, one should always be aware of the probability of overfitting datasets. The probeset name can be used to query the database resulting in a graphical representation of all expression values for a specific gene. If samples have been grouped a standard deviation bar is shown.

Figure 1: Expression values grouped by sample treatment and experiment. The extremes (blue dots), average (red dots) and STD are shown for gene 19013 (mouse: probeset 19013_at).

Mailing lists

This project provides the following mailing lists.

•  nugoctdwebapp-users: a list intended for general discussion on the project.
•  nugoctdwebapp-commits: a list that receives source code commit messages.
•  nugoctdwebapp-devel: a list intended for discussion among developers (subscription is restricted to registered developers).

Source access

If available, anonymous readonly subversion access works as follows:

  svn co https://trac.nbic.nl/svn/nugoctdwebapp nugoctdwebapp

Write access is only available to registered developers.

You can become a developer by  registering yourself if you haven't already done so, and requesting write access on the  nugoctdwebapp-users mailing list.

Starting Points

• TracGuide -- Built-in Documentation
• TitleIndex -- A complete list of local wiki pages.
•  Trac FAQ -- Frequently Asked Questions

Other NBIC software projects

All active NBIC software projects can be accessed from the  project index.