ISAAC - InterSpecies Analysing Application using Containers

BMC Bioinformatics

Herbert Baier¹  Jörg Schultz¹ 

[1] Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg 97074, Germany

关键词: Cross-species analyses;    Explorative analyses;    Gene sets;    Teamwork;   

Others  :  1087649
DOI  :  10.1186/1471-2105-15-18

 received in 2013-07-26, accepted in 2014-01-10,  发布年份 2014

【 摘 要 】

Background

Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large scale analysis. Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories.

Results

To fill this niche, we have developed ISAAC, the InterSpecies Analysing Application using Containers. The central idea of this web based tool is to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. Furthermore, one can easily switch back to previous states and perform new analyses. Currently, sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. As todays research usually is performed in larger teams and consortia, ISAAC provides group based functionalities. Here, sets as well as results of analyses can be exchanged between members of groups.

Conclusions

ISAAC fills the gap between primary databases and tools for the analysis of large gene lists. With its highly modular, JavaEE based design, the implementation of new modules is straight forward. Furthermore, ISAAC comes with an extensive web-based administration interface including tools for the integration of third party data. Thus, a local installation is easily feasible. In summary, ISAAC is tailor made for highly explorative interactive analyses of gene, transcript and protein sets in a collaborative environment.

【 授权许可】

   
2014 Baier and Schultz; licensee BioMed Central Ltd.

【 图 表 】

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