Background
The ability to visualize and manage protein-protein interaction (PPI) networks is extremely useful in biochemistry and other related research fields. Several online web servers are currently being used for these purposes. For example, the STRING database [1,2] not only provides PPI information for many organisms, but also graphically shows interactions of interest. The PINA database [3] is another online web server containing PPI information for six organisms and is also highly useful in this regard [4]. Both of these systems allow users to download PPI information they have collected from databases. However, users often experience difficulties in editing such collected information, as well as in constructing and sharing integrated PPI networks. The aim of this cisPath package is to simplify all of these processes. With cisPath, users can combine PPI information downloaded from different databases, add private data to these combinations, and construct new and personalized PPI networks. The functions available in this package are listed in Table 1.
Table 1  Functions of this cisPath Package.   In recent years, cloud applications in which application software and all associated data are hosted centrally on the cloud have become more and more popular [5-7]. Cloud users typically access the software and data via a thin client web browser. RStudio [8] which was developed by RStudio Inc. and is available under a free software license for academic use is a powerful integrated development environment for R programming language. Deploying RStudio and R on a cloud server allows primary users to provide R as a cloud application to authorized users, who can access this R workspace from any computer. In this case, only primary users need to install and update R and related packages. Using R as a cloud application provides many benefits, but the necessity of downloading output to a local machine is an inconvenience that diminishes the benefit of the cloud model. Taking this into consideration, cisPath displays all of the results in web format. As such, using this package as a cloud application allows users to visualize, manage, and share results through the web browser, instead of downloading them. For users who may have only cloud drivers, such as Google Driver instead of cloud computing servers, results can be uploaded to cloud drivers, which can then be visualized and shared via a browser. Details on how to use Google Driver in hosting online results can be found on our website [9].