Resource: Turning databases and tools into web resources with GreenMamba

Today, the users of bioinformatics databases and tools increasingly rely on being able to access them through web interfaces. Almost all major databases and most of the commonly used tools can be accessed in this manner, which is mostly good news from the users perspective. However, in my experience from teaching on numerous courses, these users have never worked with a command line and thus typically run their head against a wall the moment they have to do anything slightly more specialized than, for example, running a BLAST search or making a multiple alignment.

The reason for this is simple: specialist tools and databases are typically not made available through user-friendly web interfaces, because they have too few users to make it worthwhile to create such an interface. Worse yet, the tools are in many cases not even distributed, because the many dependencies and lack of documentation would result in too many questions if one were to distribute it. Consequently, almost every bioinformatician that I have spoken about this has one or more resources that they are currently not sharing – not because they are not willing to share, but because sharing would imply too much extra work. To address this problem, we have developed a web server that allows you to easily wrap existing databases and tools with a web interface like the one shown below.

In my group we are involved in the development and maintenance of many bioinformatics web resources, and I have thus been pushing the development of a reusable infrastructure. The result of this is the Python framework Mamba, which has primarily been developed by Sune Frankild and myself. Briefly, Mamba is a network-centric, multi-threaded queuing system that deals with the many technical aspects related to network communication with the clients and server-side resource management. All the specific work pertaining to a resource is done by modules that run under the Mamba server. GreenMamba is one such Mamba module, which based on a simple configuration file can provide a complete web interface around a tab-delimited data file or a command-line tool.

It is thus with great pleasure that we can now release the first version of the Mamba queuing system and GreenMamba wrapper under the BSD license. We hope that by eliminating most of the work in setting up bioinformatics web resources, it will encourage people to make available data sets and tools that hitherto were not worthwhile the time and effort to set up.

Over the next days and weeks, I plan to publish a series of blog posts that illustrate how one can use this framework to wrap a web interface around existing databases and command-line tools with practically no work. Impatient people are welcome to download the software and look in the greenmamba/examples directory.

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