User:Ilya

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(Activities)
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*[[User:Ilya/SocialNetworking| Social networking]]
*[[User:Ilya/SocialNetworking| Social networking]]
*[[User:Ilya/Blogging|Blogging]]
*[[User:Ilya/Blogging|Blogging]]
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===Software development===
 
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[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBricks aligner] - aligns sequence reads (fragments) to Biobrick sequence
 
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*[http://bioinformatics.ubc.ca/resources/tools/index.php?name=sim4 Sim4] is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
 
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*[[doi:10.1101/gr.8.9.967|A computer program for aligning a cDNA sequence with a genomic DNA sequence]] ([http://www.genome.org/cgi/content/full/8/9/967 backup link])
 
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*[http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/Alignment/Sim4.pm Bio::Tools::Run::Alignment::Sim4] - wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
 
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*[http://search.cpan.org/~birney/bioperl-1.4/Bio/SearchIO/sim4.pm Bio::SearchIO::sim4] - parser for Sim4 alignments
 
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*[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Exon.pm Bio::Tools::Sim4::Exon] - a single exon determined by an alignment
 
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*[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Results.pm Bio::Tools::Sim4::Results] - results of one Sim4 run
 
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*[http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-run/Bio/Tools/Run/Alignment/Sim4.pm Sim4.pm] - CVS log (latest version)
 
===Lab computing===
===Lab computing===
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*[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
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*[[User:Ilya/BioBrick aligner|BioBrick aligner]]
*[[Endy:Data storage|Data storage]]
*[[Endy:Data storage|Data storage]]
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*[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
==Notes==
==Notes==

Revision as of 16:52, 28 June 2007


Ilya Sytchev (Илья Сычёв) is a graduate student in Bioinformatics at Northeastern University working in Endy Lab at MIT.

Contact: ilyas@mit.edu

Contents

Research

Current

Previous

Mating pheromone response pathway analysis across yeast and related species

Activities

OpenWetWare

Lab computing

Notes

Synthetic Biology

Software

  • 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)
  • Babel - convert between various formats (Excel, JSON, N3, RDF/XML, etc)
  • Web 2.0-style buttons

Data visualization

  • Many Eyes - a site for sharing and commenting on visualizations by IBM
  • Data360
  • Swivel: YouTube for data - visualize and share your data with others

Application servers

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

Miscellaneous

  • MIT proxy: a bookmarklet to redirect your current browser page through MIT's Proxy, useful for browsing ACM Portal, etc. Drag it to your bookmarks toolbar, and click it on any page to view that page through the MIT proxy (via Jonathan Ragan-Kelley)
  • DNA Art
  • DNA 11
  • WEB2DNA
  • Genome Quilts - a way of encoding genetic information in quilt designs
  • FooPlot - online graphing calculator

Locations of visitors to this page

Personal tools