ISAAC - InterSpecies Analysing Application using Containers
ISAAC - InterSpecies Analysing Application using Containers
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DOI：
10.1186/1471-2105-15-18
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发表时间：
2014-01-15
影响因子：
3
通讯作者：
Schultz, Joerg
中科院分区：
文献类型：
--
作者：
Baier, Herbert;Schultz, Joerg
背景：关于基因、转录本和蛋白质的信息分布在各种各样的数据库中。使用这些数据库开发了不同的工具，以从大规模分析中识别基因列表中的生物信号。大多数情况下，他们寻求特定功能的丰富。但是，这些工具不允许探索性地浏览不同的视图，也不允许根据最新的故事改变基因列表。结果：为了填补这个空白，我们开发了ISAAC，使用容器的物种间分析应用程序。这个基于网络的工具的中心思想是能够在不同的生物学观点下分析基因、转录本和蛋白质的集合，并在分析的任何点交互地修改这些集合。详细的历史记录和快照信息允许跟踪每个操作。此外，人们可以很容易地切换回以前的状态并执行新的分析。目前，可以在基因组，蛋白质功能，蛋白质相互作用，途径，调节，疾病和药物的背景下查看集合。此外，用户可以通过现有基因集的自动、基于正字法的翻译在物种之间切换。由于今天的研究通常是在更大的团队和联盟中进行的，ISAAC提供了基于小组的功能。在这里，集以及分析结果可以交换groups.Conclusions成员之间：ISAAC填补了主要数据库和大型基因列表分析工具之间的差距。凭借其高度模块化、基于JavaEE的设计，新模块的实现非常简单。此外，ISAAC还提供了一个广泛的基于Web的管理界面，包括用于集成第三方数据的工具。因此，本地安装是容易可行的。总之，ISAAC是为在协作环境中对基因、转录本和蛋白质集进行高度探索性的交互式分析而量身定制的。
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.