Genome Networking

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This site documents the work evaluating technologies for transferring genomes to the CBSE-managed TCGA archive site.

For current status see the {{:paper.pdf|LATEST REPORT}}.

Recent presentation on this project, made for CE-280N  {{:ce-280n_presentation.ppt|LATEST PRESENTATION}}.

The plan for this evaluation site is as follows:

  * Setup a [[http://www.perfsonar.net|perfSONAR]] node at UCSC to monitor paths to TCGA-related destinations around the Internet.
  * Setup a testbed using the [[http://info.iet.unipi.it/~luigi/dummynet/|Dummynet]] tool that simulates queue and bandwidth limitations, delays, packet losses, and multipath effects.

Additional reference information can be found at:

  * ESnet's [[http://fasterdata.es.net/|fasterdata]] site.
    * An interesting [[http://fasterdata.es.net/assets/fasterdata/Dart-tutorial.pdf|presentation]] on this site at the Internet2 Joint Techs conference in 2010 by Eli Dart of ESnet.
  * Pittsburgh Supercomputing Center's site on [[http://www.psc.edu/networking/projects/tcptune/|Enabling High Performance Data Transfers]].
  * [[http://www.web100.org/|Web100 Project]]
  * Presentation on the [[http://www.es.net/assets/Uploads/20110201-dart-science-dmz.pdf|Science DMZ]] concept.

The 3 tools we are planning the test are:
^ Tool      ^ Installation ^  Results ^
| [[http://globus.org/toolkit/docs/3.2/gridftp/|GridFTP]]    | [[GridFTPInstall|Installation]]     | [[GridResults|Results]] |
| [[http://monalisa.cern.ch/FDT/|Faster Data Transfer]]    | [[FDTInstall|Installation]]| [[FDTResults|Results]] |
| [[http://genome.ucsc.edu/admin/git.html|paraFetch]]    | [[paraFetch|Installation]]     | [[ParaResults|Results]] |

Experiment Details:
  - [[ScenarioProposal| Scenario Proposal]]
  - [[Locations | Remote Locations]]
  - [[TcpTuning | TCP Tuning]]
  - **perfSonar Sites:** [[http://ndb1.internet2.edu/perfAdmin/directory.cgi|Directory]]

^ Sites      ^ PerfSONAR ^
| Sequencing Center at Washington University, St Louis    | [[WUperfSonar|Results]]     | 
| Sequencing Center at Baylor College of Medicine, Houston    | [[BCperfSonar|Results]]|
| Broad Institute, Boston    | [[BIperfSonar|Results]]     |
| University of North Carolina Sequencing Center    | [[UNCperfSonar|Results]]     |
| University Of British Columbia Sequencing Center    | [[UBCperfSonar|Results]]     |

**Data sites:**
    * [[http://hgdownload.cse.ucsc.edu/downloads.html|UCSC Genome data download page]]
    * [[ftp://hgdownload.cse.ucsc.edu/goldenPath/|FTP site:UCSC Genome data]]

Related research:
  - [[http://bioftp.org/index.php/Korean_Reference_Genome_data| KOREF Human Genome]]
  - [[http://portal.acm.org/citation.cfm?id=1592576|VL2: A Scalable and Flexible Data Center Network]] : [[VL2Notes|Notes]]
  - [[http://portal.acm.org/citation.cfm?id=956993.957002&coll=DL&dl=ACM&CFID=16657217&CFTOKEN=91943640|Web100: Extended TCP Instrumentation]]: [[Web100|Notes]]
  - [[http://research.microsoft.com/en-us/um/people/maheshba/papers/thesis.pdf|RELIABLE COMMUNICATION FOR DATACENTERS]]: [[DCNotes|Notes]]
  - [[http://nar.oxfordjournals.org/content/early/2011/01/25/nar.gkr009.full.pdf+html|Genome Compression]] : [[GCNotes|Notes]]
  - TCP Variants:
  * [[http://www4.ncsu.edu/~rhee/export/bitcp/cubic-paper.pdf|TCP Cubic Variant]]: [[Cubic|Notes]]
  * [[ftp://ftp.cs.arizona.edu/xkernel/Papers/vegas.ps|TCP Vegas]] : [[Vegas|Notes]] 
  * [[http://gridftp.bio-mirror.net/biomirror/|Bio Mirror (uses GridFTP + UDT)]]
  * [[http://www.ogf.org/OGF22/materials/1144/gridftp-ogf22.ppt|Open Grid Forum - Presentation on GridFTP]]
  * GridFTP:
    * [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.97.8734&rep=rep1&type=pdf| The Globus Striped GridFTP Framework and Server]]
    * [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.109.1941&rep=rep1&type=pdf|Globus GridFTP: What’s New in 2007]]
    * [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.138.6285&rep=rep1&type=pdf|The Globus eXtensible Input/Output System (XIO)]]
    * [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.58.4783&rep=rep1&type=pdf| Internet Congestion Control for Future High Bandwidth-Delay Product Environments]]
  * UDT:
    * [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.113.5963&rep=rep1&type=pdf| UDT: UDP-based Data Transfer for High-Speed Wide Area Networks ]]
Other links:
  * [[http://www.dokuwiki.org/syntax|Wiki Syntax]]
Genome Networking

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