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Nick Reppe

 

Project Summary:An implementation of

CyVerse provides life scientists with a powerful computational infrastructure to handle huge datasets and complex analyses that enable data-driven discovery. CyVerse's extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, APIs, and more.


 

The Discovery Environment (DE) is a key product of the CyVerse cyber-infrastructure, providing a modern web interface for powerful computing. The visual and interactive computing environment (VICE) is the recently introduced feature within CyVerse’s Discovery Environment (DE) for running interactive apps.

 

Our midterm project is an implementation of CyVerse's Discovery Environment using an app we created via VICE in within CyVerse. 


Project Description


Code Availability


Initial Scripts:

https://github.com/KartinJulia/SequenceServer

 

Sequences used were provided by Team BlastEasy :

https://github.com/raptorslab/blastEasy/tree/master/queryseq



Installing/Running Instructions

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The running analysis was accessed which allowed us to paste the protein sequences in Sequence Server to run BLAST:





Conclusions: Sequence server ran on the same set of protein sequences and database on 1, 2, 4 and 8 cores. A All protein sequences ran through Sequence Server were 100 residues in length and the number of cores were pre-selected before launching the app analysis. A significant decrease in run-time was observed as more cores were involved in running queries. Running queries on 8 cores clearly reduces run-time as compared to running queries on simply 1 core. 

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Number of Protein Sequences

Time (seconds)

1 CORE

Time (seconds)

2 CORES

Time (seconds)

4 CORES

Time (seconds)

8 CORES

1303.92820.125510.12450.8775
5528.6138273.5522171.6486222.3423
108513.1129395.6723243.6747293.5924
5049145.972826419.4118313.235923710.0300
10048884.248637434.115825518.753932120.8741
5001171427.7194646156.757293580.8774942119.2246

 

 

Presentation

https://docs.google.com/presentation/d/1D755s013X6MVVlTszQXayMuy0A3CpYIpEdLfHAsX_ig/edit?usp=sharing

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