SPOT-ITN-BIOINFOrmatics

IRP8, the research projects defined in the Solanaceae Pollen Thermotolerance-Initial Training Network (SPOT-ITN) funded by Marie Curie Actions, aims to the "Development of a Gene Network for Modelling Pollen Thermo-tolerance". The related activities are mainly focusing on the set up of suitable bioinformatics, covering the following objectives: 1) development of an efficient data management system; 2) implementation of suitable methods for data processing; 3) comparative analyses among heat sensitive and tolerant genotypes. The main final goals are 4) attempting to identify genes implied in the heat shock response, possibly inferring on the involved regulatory networks and 5) establishing standards for data exchange and integration to find the most adequate reconciliation of resources from different information levels that describe the biological response.

This portal is accessible only to registered users and is specifically dedicated to the SPOT-ITN bioinformatics. At this stage, this SPOT-ITN dedicated portal entails six different cross-linked platforms, enriched with publicly available data and the private data provided by the SPOT-ITN partners of the project. Among all, four different platforms and services are ready to be exploited in a preliminary release.

Data Accessibility

At the moment, each user (SPOT-ITN member or registered public user) can refer to the register webpage to request a personal access permission. In general, all users are asked to register to declare their identity for further tracing and system evaluation issues. After registration, each user will receive a confirmation email in terms of account activation with the dedicated permission to his/her working area. All users have access to the publicly available data. Private data is also accessible, only and if only, the data are confirmed to be accessible to this group officially by the data provider supported by a role base system (responsible of the data will be informed accordingly to give their permission).

This means that no private data can be accessed without a full agreement with the data provider.

Data Sharing Platform

Each user can provide data in any format (RAW, Cleaned and analyzed) using the upload page by providing detailed information about the experiment and type of analysis made on the data. The data will be then integrated into the system according to the role base policies mentioned.

Genome Browser Platform

Genome Browser (GB) is an open source platform for visualization of tracks data along the genome for genome wide investigations. The platform has been already set up for Tomato and the available "omics" data such as (iTAG official annotation, Expressed Sequence tags (ESTs), Tentative consensuses (TCs), transcriptomic indices from SGN, PlantGDB and DanaFarber) are included. Moreover, the NGS data (Heinz Library from Nature paper and MACE data from SPOT-ITN partners) are also included.

Expression Platform

Expression platform is the first expression database for tomato entailing NGS data. It is a platform designed to provide users full support to query Gene Expression of tomato genes based on different sets of criteria (e.g. exon/intron base, raw/normalized/log2 transformed and ID/functional keyword query base). The platform provides different insights to the expression analysis for the users, and facilitate the comparative analysis of gene expression based on the available libraries under role based policies defined in data accessibility section. Moreover, the platform is cross-linked to the Genome Browser platform for further investigations. At the moment the platform can be exploited for investigations of MACE based analyses.

Tomato Genome Platform

Tomato Genome Platform is a dedicated genome platform to investigate the tomato genome annotations. This platform enables the genome wide investigation by ID or functional keywords using customized queries. While the platforms are in the preliminary public release, your feedbacks and criticisms are really welcome to fix possible bugs and mistyping, to request for support or solve any other inconvenient event in the system. Please consider that we are still completing the upgrading of the hardware system to fully technically support an extended usage of the service herein provided.

A downloadable instruction page to exploit the platform is also available in the website under the help section.

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