Difference between revisions of "User:Ilya"

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Ilya Sytchev (Илья Сычёв) is a graduate student in [http://www.bioinformatics.northeastern.edu/ Bioinformatics] at [http://www.northeastern.edu/ Northeastern University] working in [[Endy|Endy Lab]] at [http://mit.edu/ MIT].
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__NOTOC__
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Contact Ilya Sytchev (Илья Сычёв):
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*<math>\mbox{hackdna}</math>@<math>\mbox{gmail.com}</math>
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*[[Special:Emailuser/Ilya|send me an email via OpenWetWare]]
  
Contact: <math>\mbox{ilyas}</math>@<math>\mbox{mit.edu}</math>
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==Activities==
 
 
==Research==
 
  
 
===Current===
 
===Current===
*[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for the [http://parts.mit.edu/ Registry of Standard Biological Parts]
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Developing an integrated data management and analysis system for the [http://winhide.wordpress.com/2011/04/13/setting-up-a-stem-cell-commons/ Stem Cell Commons] project.
**[[Synthetic_Biology:Semantic_web_ontology/Notes|Notes]]
 
  
 
===Previous===
 
===Previous===
[[Yeast:Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[Yeast|yeast]] and [[Yeast:Phylogeny|related species]]
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*Systems Engineer at [http://www.genstruct.com/ Genstruct]
 
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*[[User:Ilya/OpenWetWare|OpenWetWare]]
==Activities==
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*Computing at the Endy Lab:
 
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**[[User:Ilya/BioBrick aligner|BioBrick aligner]]
===OpenWetWare===
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**[[Endy:Data storage|Data storage]]
[[User:Ilya/OpenWetWare|Notes]]
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**[[User:Ilya/Lab network|Lab network]]
 
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**[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
===Software development===
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*[[User:Ilya/Yeast/Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[User:Ilya/Yeast|yeast]] and [[User:Ilya/Yeast/Phylogeny|related species]]
[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBricks aligner] - aligns sequence reads (fragments) to Biobrick sequence
 
*[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
 
*[[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])
 
*[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
 
*[http://search.cpan.org/~birney/bioperl-1.4/Bio/SearchIO/sim4.pm Bio::SearchIO::sim4] - parser for Sim4 alignments
 
*[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Exon.pm Bio::Tools::Sim4::Exon] - a single exon determined by an alignment
 
*[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Results.pm Bio::Tools::Sim4::Results] - results of one Sim4 run
 
*[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===
 
*[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
 
*[[Endy:Backup_solutions|Data backups]]
 
 
 
==Notes==
 
*[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
 
*[http://biology-pages.info/ Kimball's Biology Pages]
 
*[[Bioinformatics]] @ OpenWetWare
 
*[[Computing/Web2.0|Web 2.0]]
 
*[[User:Ilya/Digital_evolution|Digital evolution]]
 
*[http://web.mit.edu/network/ MIT Network and Infrastructure Team] - network maps, etc
 
*[[User:Ilya/IAP|IAP]]
 
 
 
===Synthetic Biology===
 
*[[SB:FAQ|Synth Bio FAQ]]
 
*[http://www.dnahack.com/ DNA Hack] - The website for Amateur Genetic Engineering
 
*[[Synthetic_Biology:Press|Press]]
 
*using analog circuits/logic
 
**digital design is modular and predictable (abstraction hierarchy)
 
**[[Reshma_Shetty/FAQ_and_thoughts|Reshma's thoughts]]
 
**[http://web.media.mit.edu/~vigoda/phd/phd.htm Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing] by Ben Vigoda
 
**[[Wikipedia:Analog_circuit|Analog circuit]] Wikipedia article
 
**[http://kabuki.eecs.berkeley.edu/ Research in analog IC design]
 
**[http://www.falstad.com/circuit/ Circuit simulator applet]
 
**[http://www.circuitsage.com/ Analog design resources]
 
**[http://zone.ni.com/devzone/conceptd.nsf/webmain/D59654FA44D2F9FA86256F4A006064F3 Basic Analog Circuits - Tutorial]
 
*Cell-free synthetic biology
 
**[[doi:10.1126/science.1132493|Enzyme-Free Nucleic Acid Logic Circuits]], Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree
 
**[[doi:10.1126/science.1135101|Perspectives essay in Science: Pulling Strings]], Walter Fontana
 
**[http://www.nature.com/msb/journal/v2/n1/full/msb4100099.html Construction of an in vitro bistable circuit from synthetic transcriptional switches], Jongmin Kim, Kristin S White and Erik Winfree
 
**[http://www.nature.com/msb/journal/v2/n1/full/msb4100104.html Cell-free synthetic biology: a bottom-up approach to discovery by design], Michael L Simpson
 
 
 
===Software===
 
*[http://wwwhomes.uni-bielefeld.de/chase/biotool2web/ Biotool2Web]: Creating Simple Web Interfaces for Bioinformatics Applications
 
*[http://modis.ispras.ru/sedna/index.htm Sedna] is an open source XML-native database management system developed from scratch in C/C++ and Scheme
 
*[http://www.aggregatedata.com/ Aggregate Data] utilizes AJAX-based "sliders" so survey takers can choose anywhere along a spectrum of opinion
 
*CHM file viewers for non-Windows platforms
 
**[http://gnochm.sourceforge.net/ GnoCHM]
 
**[http://xchm.sourceforge.net/ xchm]
 
**[http://chmox.sourceforge.net/ Chmox] - a Mac OS X CHM viewer
 
*[http://tor.eff.org/ Tor]: an anonymous Internet communication system
 
*[http://wireshark.org/ Wireshark]: network protocol analyzer (successor to [http://www.ethereal.com/ Ethereal])
 
*[http://www.swivel.com/ Swivel]: YouTube for data - visualize and share your data with others
 
*[http://services.alphaworks.ibm.com/manyeyes/home Many Eyes] - a site for sharing and commenting on visualizations by IBM
 
*[http://simile.mit.edu/babel/ Babel] - convert between various formats (Excel, JSON, N3, RDF/XML, etc)
 
*[http://iris-design.info/photoshop/web-20-style-buttons/ Web 2.0-style buttons]
 
 
 
===Application servers===
 
*[http://www.whitebeam.org/ Whitebeam] - open source; applications are written as a set of XML pages that contain embedded JavaScript
 
[[Category:Steering Committee member]]
 
[[Category:People at MIT]]
 
 
 
===Miscellaneous===
 
*[http://www.dnaartistry.com/ DNA Art]
 
*[http://www.dna11.com/ DNA 11]
 
*[http://www.baekdal.com/web2dna/ WEB2DNA]
 
  
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==Miscellaneous==
 
<html>
 
<html>
<a href="http://www2.clustrmaps.com/counter/maps.php?url=http://openwetware.org/wiki/User:Ilya" id="clustrMapsLink"><img src="http://www2.clustrmaps.com/counter/index2.php?url=http://openwetware.org/wiki/User:Ilya" style="border:1px solid;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onError="this.onError=null; this.src='http://clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://clustrmaps.com'" />
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<a href="http://www2.clustrmaps.com/user/3e416041">
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<img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" />
 
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*[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for [[Synthetic Biology]] ([[User:Ilya/Registry|Registry notes]])
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*[[User:Ilya/Notes|Notes]]
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*[[User:Ilya/Todo|Todo]]
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*[[User:Ilya/Sandbox|Sandbox]]
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[[Category:Steering Committee member]] [[Category:Bioinformaticians]]

Latest revision as of 17:35, 28 October 2012

Contact Ilya Sytchev (Илья Сычёв):

  • Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \mbox{hackdna}} @Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \mbox{gmail.com}}
  • send me an email via OpenWetWare

Activities

Current

Developing an integrated data management and analysis system for the Stem Cell Commons project.

Previous

Miscellaneous

<html> <a href="http://www2.clustrmaps.com/user/3e416041"> <img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" /> </a> </html>