Bio IT World Expo 2016  
Bio IT World Expo 2016

Workshop Details

Running a Local Galaxy Instance
Tuesday, April 29, 2014 | 12:30 – 4:00 pm


Galaxy is one of the most popular open-source platforms for biomedical data analysis because it enables many complex computational tools to be accessible to scientists with little bioinformatics and programming capabilities. Many organizations choose to host their own Galaxy instances to enable customization of Galaxy to their own needs. However, it can be challenging to choose the correct infrastructure to host Galaxyand configure Galaxy to run efficiently. This workshop will discuss some of the challenges and describe the best practices for installing and managing your own Galaxy instance.

Please bring a laptop to follow along with the tutorial. 


12:30 pm Organizer’s Welcome and Chairperson’s Opening Comments

12:45 Introduction to Local Galaxy

  • Overview of Galaxy
  • Why a Local Galaxy Instance

1:15 Setting up a Local Galaxy Tutorial (Part I)

  • Basic installation of an instance
  • Using the Toolshed
  • Setting up Genomes

2:00 Refreshment Break

2:15 Optimizing Local Galaxy

  • Best practices for running a production Galaxy

3:00Setting up a Local Galaxy Tutorial (Part II)

  • Optimizing Local Galaxy

3:45 Interactive Q&A and Session Wrap-up

4:00 End of workshop


Adam Kraut, Senior Scientific Consultant, BioTeam

Adam is a Senior Scientific Consultant at BioTeam with ten years of bioinformatics experience. Prior to BioTeam, Adam was a computational biologist at the Pittsburgh Supercomputing Center specializing in Protein Structure and Function. Since joining BioTeam Adam has focused on High Performance Computing and Cloud Computing for science and engineering. He is an active speaker at Bio-IT conferences and passionate about building agile research computing infrastructures.

Nate Coraor, System Administrator, Galaxy Team

Nate is a system administrator, programmer, and a part of the Galaxy Team at Penn State University. His primary contributions to the project are to the infrastructure architecture and maintenance for the Public Server and programming related to systems tasks such as running jobs.

Anushka Brownley, Senior Scientific Consultant, BioTeam

Anushka studied Computer Science at Carnegie Mellon University before receiving her Masters in Bioinformatics from Georgia Institute of Technology. She has spent the last ten years working in NGS with a focus on building bioinformatics pipelines for data management, analysis, and interpretation of genome sequence data. At the J. Craig Venter Institute, she used open-source and proprietary code to implement both production and customized systems to manage and analyze data from targeted re-sequencing of human, bacterial, viral, and synthetic genomes. She then worked at Complete Genomics doing bioinformatics analysis of whole human genome sequence data to help develop the internal genome assembly processes and final product for the sequencing-as-a-service company. Subsequently, Anushka transitioned to Product Management to spearhead the Complete Genomics Cloud project and also managed their open-source analysis software tool suite. She is particularly interested in understanding the broad range of scientific computational needs and building relevant and efficient solutions that produce actionable information.

Tristan Lubinski, Consultant, BioTeam

Tristan received a Bachelor of Arts degree in Computer Science from Luther College and a Bachelor of Arts degree in Biology from Lakeland College before performing research in yeast genetics at Boston College and enrolling in the Graduate Biology program at Boston University. At Boston University he is a member of the Finnerty Lab and has been studying the evolution of the NF-kB stress response pathway in the basal marine organism Nematostellavectensisthrough the use of Next-Generation sequencing technology and design and development of computational methods to investigate gene regulatory networks. Tristan joined The Bioteam in the summer of 2013 as a consultant where he is currently focused on aiding in the development of the Slipstream Galaxy Appliance.

James Reaney, Senior Director, Research Markets at SGI
James Reaney has over seventeen years experience as an IT Manager and computing/networking/storage analyst in various HPC research environments. Prior to joining SGI Dr. Reaney was a Director for Hitachi Data Systems’ Healthcare & Life Sciences business segment, and he also created and led the Research Markets business segment for BlueArc Corporation.  Earlier in his career Dr. Reaney was Network & Server Operations Manager for the Life Sciences at Harvard University, where he helped architect and build various computing solutions to support both the academic and research missions of the faculty. Today Dr. Reaney visits research computing environments worldwide to help others in the community better design and implement their own solutions.  His experience provides him with a solid working knowledge of research customers' day-to-day operations, the challenges faced by local IT staff, how to better meet the fiscal requirements of research administrations, and how the SGI family of products help accelerate and scale research projects while making life a little easier to manage for the IT administrator. 


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