Introduction

Basics

Our application was originally designed to help CeGen users to handle, retrieve, transform and analyze the genetic data generated by the genotyping facilities of the institution. Hoewever, SNPator is also open to external users who may want to upload their own genotyped data in order to take advantage its data processing features.

Users, depending on their interests, will be able to perform a set of operations which may range from very simple format transformations (e.g. creating input files from their data for different bioinformatics software) to some complex biostatistical calculations that may help them to mine their datasets without having to be familiar with the statistical software usually involved in such studies.

Support to users is offered together with the commitment by Spain's National Institute for Bioinformatics of maintaining the application running, up to date and publicly available.

Studies

The data needed to perform the analysis capabilities we offer is stored in our database and organized in different sets called "studies".

A Study consists of:

  1. A set of samples (generally individuals) with associated information about sex, age, disease or whatever features that the user may consider important in order to characterize samples. The information included here can be as exhaustive as needed and, of course, may be completely absent in cases where only genomic studies (e. g. linkage disequilibrium) are the goal.
  2. A set of SNPs with associated genomic information (e. g. chromosome position). As in the case of studies, this information can be as exhaustive as desired by the user or at all absent.
  3. The results obtained by genotyping the selected SNPs in the selected samples. This data usually comes from the high-throughput genotyping facilities of CeGen or the user's own lab, but other sources of data are possible (e.g. HapMap).

Users

Access to the data is obviously restricted. Users and Groups of users are defined by the system in order to guarantee data confidentiality. Each user or group is allowed to access a list of studies and to operate with the data included in them.

The operations that a user may perform are also restricted. Each user is assigned to one of the following roles:
Browser Data browsing and operations.
Editor Uploading and modification of SNPs, Sample and Results data.
Designer Creation of new customized fields for the characterization of SNPs and samples.
Administrator The application administrators are responsible for maintaining the system and must be contacted in case some change is needed.