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Galaxy

Galaxy. Presented by Leshi Chen. Project Overview. Upgrade current biology python codes to Object Orientation Wrap python codes as well as perl codes to became Galaxy Module Set up a Galaxy web server to share tools developed by PFR. Project Overview cont.

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Galaxy

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  1. Galaxy Presented by Leshi Chen

  2. Project Overview • Upgrade current biology python codes to Object Orientation • Wrap python codes as well as perl codes to became Galaxy Module • Set up a Galaxy web server to share tools developed by PFR

  3. Project Overview cont. • PFR developing a Galaxy server is aimed to help: • Biologist, scientist to share their knowledge and use the tools published by Galaxy to analyze multiple alignments, compare genomic annotations, profile metagenomic samples and so on. • Low tech labs can use the Galaxy to analyze their gene sequence by using current tools developed by PFR. Galaxy can reduce their research cost.

  4. What is Galaxy --- Concept • Galaxy is a framework for integrating computational tools. It allows nearly any tool that can be run from the command line to be wrapped in a structured well defined interface. • Galaxy provides an accessible environment for interactive analysis that transparently tracks the details of analyses. A workflow system for convenient resue, data management and sharing.

  5. What is Galaxy cont..

  6. What is Galaxy --- Interface

  7. What is Galaxy --- Interface • Input • Source file or Source data • Options such as range of SNP • Output • Data

  8. What is Galaxy --- Output

  9. Current work: • Improvement existing python code • A class called PFR_GFF to dealing with Gff file format • Convert 454AllDiffs + fasta to gff3 • Convert gff3 + fasta to genbank file (gb) • Read gff3 file into sequence record dictionary • Wrap the class into Galaxy Module • Wrap MISA.PL into Galaxy Moduel

  10. Current work:

  11. Output Sample ---GenBank

  12. Output Sample ---MISA.PL

  13. Reference • [1] Bitbucket, 2010, http://bitbucket.org/galaxy/galaxy-central/wiki/Home • [2]Galaxy Screencasts, The best way to understand how.., 2010, http://main.g2.bx.psu.edu/screencast

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