Garuda Workshop - Re-imagining Connectivity in Biology and Medicine

Dates: 15 & 16 May 2017

Venue: Gini hall - Building CU002, Dept. of Statistical Sciences, Università degli Studi di Roma "La Sapienza" , Piazzale Aldo Moro 5, 00185 Roma, Italy.

Organizers: Bioinformatics course (Prof P. Tieri, F. Cincotti), Laurea Magistrale in Data Science, La Sapienza University of Rome & The Systems Biology Institute, Tokyo, Japan & CNR IAC Istituto per le Applicazioni del Calcolo, Rome, Italy.


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With the explosion of data in different dimensions of drug discovery, biomedicine and healthcare, a key challenge is the ability to connect the disparate data sources, discover the right analytics tools for a specific analysis and navigate through inter-operable analytics to provide executable insights. Garuda is an open, community-driven, platform that provides a framework to discover, connect & navigate through different applications on devices as well as in the cloud.

Through this workshop, we will provide an overview of Garuda platform, the alliance eco-system and a brief demonstration of the platform in action together with its various components. The demonstration is specifically designed to cater to an array of audience from different backgrounds with a goal towards re-imagining connectivity and integrated analytics in biomedical research, healthcare and beyond.

Attendance is limited to 30 people. Registration is free but mandatory. Participants should bring their own computer. For futher info please contact Paolo Tieri (paolo DOT tieri AT cnr DOT it) or Vipul Gupta (vgupta AT sbi DOT jp).

Workshop Program

 

  • May 15 2017
Session 1 (9.30 am -12.30 pm): Garuda Platform introduction and demonstration of its basic architecture.
  • Session 2 (2 pm - 5pm), hands-on 1: Biological Pathway Modeling and Simulation. Attendees will learn how-to construct, simulate and manipulate biological networks in Garuda.

 

  • May 16 2017
  • Session 1 (9.30 am -12.30 pm), hands-on 2: Microarray Data Analytics. Participants will download processed microarray expression data from Open TG-GATEs (http://toxico.nibiohn.go.jp/english/) and perform enrichment analysis using gadgets such as Reactome, Biocompendium, ipath etc.
  • Session 2 (2 pm - 5pm): In the final session of this 2-day workshop, attendees will learn from Garuda Technical Lead on how to "Garudify" their tool/scripts and publish it as a "Gadget" on Garuda Gateway.

Why Garuda?

Need for a platform to connect, discover and navigate through High Dimensional (HD) Data and HD Analytics

What is Garuda?

Garuda is a connectivity platform to connect, discover and navigate through inter-operable "gadgets" with applications in biology, healthcare and beyond. Garuda provides an open interface to connect various tools (called Gadgets in Garuda) which are available through the Garuda Gateway. The platform is currently in 1.x invited beta for the community while the professional version provides client-specific “gadgets”. The current repertoire includes around 100+ gadgets.

Download Garuda

IMPORTANT INFORMATION Mac users: Due to security issues on OSX 10.7 and above, you would need to change permissions to launch Garuda. Please follow the instructions here to solve the issue. Some users reported that the above solution still does not solve the launch issue after change of permissions and may require a reboot to reflect the permission changes to use the Garuda application.

DEPENDENCIES: Mac: The current Garuda Platform requires Perl (which comes preinstalled on MacOS) and Java 1.6 or above to run on Mac. You can download the latest version of Java (JRE or JDK) from the link below. Some gadgets require Java 6 to run. It is recommended to use Java 6 for this 1.2beta version of Garuda Platform on Mac. You can download it from here.
Windows: The dependencies on Java and Perl are bundled in the Garuda installer for Windows and does not require additional installation.

How does Garuda work?

Programming language and operating system agnostic interface (APIs) which allows to "garudify" data sources, analytics tools and algorithms to power their integration and faceplate context-dependent interpretations

Garuda in Action

Some of the popular analytics videos using an array of Garuda gadgets.

What is the Garuda engagement model?

The base platform (Community) is available for free and provided by Garuda Alliance led by The Systems Biology Institute. "Gadgets" (any data, service, algorithm, tool available on Garuda platform) are provided by the original developer of the gadgets in the BYOL model (Bring your own license). "Custom gadgets" for specific clients are provided by SBX Corp and subsidiaries.