WHAT IS GARUDA?
Garuda is an open, community-driven, common platform that provides a framework to connect,
discover and navigate through different applications, databases and services in biology and medicine.
Garuda provides language independent API to connect software as gadgets,
explore them through the gateway and operate them through the dashboard, all
the while supported by a global alliance of leaders in computational biology and informatics.
The complexity of living systems entails the study of biology at multiple dimensions of time and space. In recent years, we have seen a explosion is large scale omics data which aim to capture this complexity at a systems level.
- Data - Big and Small
The availability of large experimental data sets which have high variety, variability, volume and need veracity and visualization characterize what is commonly known as biological big data.
At the same time, in order to interpret the big data , filter the signal from the noise and lead to actionable insights, researchers need to focus on the biological small data - data which leads to meaningful information and contributes to knowledge about living systems.
- Analytics Diversity
To extract meaningful information and knowledge from data, researchers need to use a diverse set of computational tools, algorithms, database and analytical services. Various computational approaches have been developed to study biological systems at the level of genes, transcripts, proteins, metabolites to cells, tissues organ and whole body modeling.
- Discoverability and Navigability
With the diverse and ever-increasing set of databases, novel algorithms, software and services been made available to the research community, a recurring question faced by researchers is-How can I discover the right tools for my data set and the scientific problem I wish to address?
At the same time, most analysis require the use of multiple database, tools and software in different context, and more often than not, it is not possible to define the set of tools and their sequence of connections a priori. Closely associated with discovery is the question of navigability -How can I navigate through the different tools, services and databases in my analysis pipeline?
- Need for a platform
The complexity and multi-dimensionality of data and analytics make it extremely challenging to develop a single, stand-alone system which can integrate diverse sets of data and analysis techniques. Instead, a platform which connects the diverse components through open interfaces, and allows the community to discover and navigate through them, can provide a unique collaborative eco-system.
HOW DOES IT WORK?
The central driving principle of Garuda is connectivity. In this, Garuda derives its inspiration from the connectivity of the Internet, which is powered by a set of protocols (like http, tcp etc.) which together form the network stack. In order to provide a simple mechanism which allows software and services to connect in a language independant manner, Garuda works on defining a core of messages, specified in a a protocol, which can be exchanged over the standard network stack.
Garuda Protocol, Core and APIs
The Garuda Protocol is set of simple messages, currently 6 core messages, which are encoded in JSON format and can be exchanged over standard network stack. The heart of Garuda is the core which provides implementation of the protocol messages and serves as a broker to send, receive and process the protocol messages. The core can run on a local machine as well as on a server. The current release of Garuda has a local core.
The Protocol and APIs are open and freely available to the community to develop their own gadgets!
The driving force of the platform are the Gadgets. Any software, analytics tool or service which implements the Garuda Protocol either through the available API SDKs or its own implementation and is able to communicate with the core becomes a Garuda Gadget.
Since the protocol is a set of messages, there is no language or system specific dependency. Developers can implement the protocol in the language of their choice, and make their gadgets discoverable by Garuda.
Gadgets can communicate with each other if they can share some common input/output (I/O) formats. Thus, a key part of a gadget is the definition of its I/O - what file types/formats can it send or receive.
Standardization of formats is central to integrate diverse data-sets and inter-operate diverse analytic tools and services, as evidenced by pioneering efforts in Systems Biology Markup Language (SBML), Systems Biology Graphical Notation (SBGN), metadata description language like ISA-Tab and many more.
At the same time, several challenges still exist in developing globally used standards in bio-medical research. Garuda follows an Open Standards approach.
Garuda does not define a set of data formats or standards. Every gadget is free to define its own I/O (inputs and output formats, file types). However, if the gadget has its unique I/O which other gadgets do not understand, it will not be discoverable in Garuda. In other words, the gadget will not be social!
Check the GadgetSocial gadget on your dashboard and see how you can build your gadget social network in the Getting Started gadget.
The Dashboard is the personal interface for users to Garuda and gadgets, from their computers. It provides one-stop access to explore the different gadgets users have installed, check their functions and get new gadgets.
Bring Your Own License
The Garuda Platform has a BYOL (pronouced "By-All") model - Bring Your Own License
Every Gadget can have their own license for the tool/database or service associated with the gadget and can specify the information on the gadget as well as the Gateway.
The Garuda Gateway, as the name suggests, is the window to all things Garuda. Accessible via the web, it allows users to explore new gadgets available and download them to their personal dashboards.
If you feel interested, please join the community and get a free invite to the Gateway [here].
JOURNEY OF THE GARUDA ALLIANCE
The power of Garuda lies in the community - the Garuda Alliance. The Garuda Alliance provides an open community for researchers, developers, students from academia and industry to bring their databases, tools and services as gadgets on Garuda, connect and collaborate. In order to solve the grand challenges in bio-medicine and health, engineering an open, community-driven framework which allows diverse set of knowledge bases, data-sets, experimental systems and analytic tools to connect and collaborate is essential. An Integrated platform and not individual systems will lead the way to the future of biology.