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| 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].
| | __NOTOC__ |
| | Contact Ilya Sytchev (Илья Сычёв): |
| | *<math>\mbox{hackdna}</math>@<math>\mbox{gmail.com}</math> |
| | *[[Special:Emailuser/Ilya|send me an email via OpenWetWare]] |
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| Contact: <math>\mbox{ilyas}</math>@<math>\mbox{mit.edu}</math>
| | ==Activities== |
| | |
| ==Research== | |
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| ===Current=== | | ===Current=== |
| [[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for the [http://parts.mit.edu/ Registry of Standard Biological Parts].
| | 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. |
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| ===Previous=== | | ===Previous=== |
| [[Yeast:Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[Yeast|yeast]] and [[Yeast:Phylogeny|related species]]
| | *Systems Engineer at [http://www.genstruct.com/ Genstruct] |
| | | *[[User:Ilya/OpenWetWare|OpenWetWare]] |
| ==Activities==
| | *Computing at the Endy Lab: |
| | | **[[User:Ilya/BioBrick aligner|BioBrick aligner]] |
| ===OpenWetWare===
| | **[[Endy:Data storage|Data storage]] |
| [[User:Ilya/OpenWetWare|Notes]]
| | **[[User:Ilya/Lab network|Lab network]] |
| | | **[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] |
| ===Software development===
| | *[[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
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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 | |
| *[[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 | |
| *[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)
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| | |
| ===Lab computing===
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| [[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] | |
| | |
| ==Notes==
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| *[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder] | |
| *[http://biology-pages.info/ Kimball's Biology Pages]
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| *[[Bioinformatics]] @ OpenWetWare | |
| *[[Computing/Web2.0|Web 2.0]]
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| *[[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
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| *[[Synthetic_Biology:Press|Press]]
| |
| *using analog circuits/logic
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| **digital design is modular and predictable (abstraction hierarchy)
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| **[[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
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| **[http://kabuki.eecs.berkeley.edu/ Research in analog IC design]
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| **[http://www.falstad.com/circuit/ Circuit simulator applet]
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| **[http://www.circuitsage.com/ Analog design resources]
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| **[http://zone.ni.com/devzone/conceptd.nsf/webmain/D59654FA44D2F9FA86256F4A006064F3 Basic Analog Circuits - Tutorial]
| |
| *Cell-free synthetic biology
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| **[[doi:10.1126/science.1132493|Enzyme-Free Nucleic Acid Logic Circuits]], Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree
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| **[[doi:10.1126/science.1135101|Perspectives essay in Science: Pulling Strings]], Walter Fontana
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| **[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
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| **[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
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| *[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
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| *[http://www.aggregatedata.com/ Aggregate Data] utilizes AJAX-based "sliders" so survey takers can choose anywhere along a spectrum of opinion
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| *CHM file viewers for non-Windows platforms
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| **[http://gnochm.sourceforge.net/ GnoCHM]
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| **[http://xchm.sourceforge.net/ xchm]
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| **[http://chmox.sourceforge.net/ Chmox] - a Mac OS X CHM viewer
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| *[http://tor.eff.org/ Tor]: an anonymous Internet communication system
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| *[http://wireshark.org/ Wireshark]: network protocol analyzer (successor to [http://www.ethereal.com/ Ethereal])
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| *[http://www.swivel.com/ Swivel]: YouTube for data - visualize and share your data with others
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| | |
| ===Application servers===
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| *[http://www.whitebeam.org/ Whitebeam] - open source; applications are written as a set of XML pages that contain embedded JavaScript
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| [[Category:Steering Committee member]]
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| [[Category:People at MIT]]
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| | |
| ===Miscellaneous===
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| *[http://www.dnaartistry.com/ DNA Art]
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| *[http://www.dna11.com/ DNA 11]
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| *[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'" /> | | <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> | | </a> |
| </html> | | </html> |
| | |
| | *[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for [[Synthetic Biology]] ([[User:Ilya/Registry|Registry notes]]) |
| | *[[User:Ilya/Notes|Notes]] |
| | *[[User:Ilya/Todo|Todo]] |
| | *[[User:Ilya/Sandbox|Sandbox]] |
| | |
| | [[Category:Steering Committee member]] [[Category:Bioinformaticians]] |
