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*[ DNA seen through the eyes of a coder]
*[ DNA seen through the eyes of a coder]
*[ Kimball's Biology Pages]
*[ Kimball's Biology Pages]
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*[[Computing/Web2.0|Web 2.0]]
*[[Computing/Web2.0|Web 2.0]]
*[[User:Ilya/Digital_evolution|Digital evolution]]
*[[User:Ilya/Digital_evolution|Digital evolution]]
*[[ MIT Network and Infrastructure Team]] - network maps, etc
===Synthetic Biology===
===Synthetic Biology===

Revision as of 17:39, 21 December 2006

Graduate student in Bioinformatics at Northeastern University working in Endy Lab at MIT.





Semantic Web Ontology for the Registry of Standard Biological Parts.


Mating pheromone response pathway analysis across yeast and related species




Software development

BioBricks aligner - aligns sequence reads (fragments) to Biobrick sequence

Lab computing


Data storage

  • MIT TSM Backup Service
    • TSM software (free to MIT community per site license)
    • Monthly service charge: $7.50 per month per computer
    • TSM software is available for Windows, Mac and Linux free from MIT
    • Backups are stored on one of the four TSM backup servers in building W91
    • Manual or Scheduled Backup
    • Old versions of current files and deleted files are kept for 30 days
    • Need a separate account for each computer to be backed up


Synthetic Biology


  • Biotool2Web: Creating Simple Web Interfaces for Bioinformatics Applications
  • Sedna is an open source XML-native database management system developed from scratch in C/C++ and Scheme
  • Aggregate Data utilizes AJAX-based "sliders" so survey takers can choose anywhere along a spectrum of opinion
  • CHM file viewers for non-Windows platforms
  • Tor: an anonymous Internet communication system
  • Wireshark: network protocol analyzer (successor to Ethereal)

Application servers

  • Whitebeam - open source; applications are written as a set of XML pages that contain embedded JavaScript


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