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]]
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Contact: <math>\mbox{ilyas}</math>@<math>\mbox{mit.edu}</math>
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==Activities==
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==Research==
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===Current===
===Current===
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*[[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.
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**[[Synthetic_Biology:Semantic_web_ontology/Notes|Notes]]
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===Previous===
===Previous===
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[[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]]
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==Activities==
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*Computing at the Endy Lab:
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**[[User:Ilya/BioBrick aligner|BioBrick aligner]]
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===OpenWetWare===
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**[[Endy:Data storage|Data storage]]
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[[User:Ilya/OpenWetWare|Notes]]
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**[[User:Ilya/Lab network|Lab network]]
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[[User:Ilya/Spamassassin|Spamassassin]]
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**[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
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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]]
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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)
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===Lab computing===
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*[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
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*[[Endy:Backup_solutions|Data backups]]
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==Notes==
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*[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
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*[http://biology-pages.info/ Kimball's Biology Pages]
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*[[Bioinformatics]] @ OpenWetWare
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*[[Computing/Web2.0|Web 2.0]]
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*[[User:Ilya/Digital_evolution|Digital evolution]]
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*[http://web.mit.edu/network/ MIT Network and Infrastructure Team] - network maps, etc
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*[[User:Ilya/IAP|IAP]]
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===Synthetic Biology===
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*[[SB:FAQ|Synth Bio FAQ]]
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*[http://www.dnahack.com/ DNA Hack] - The website for Amateur Genetic Engineering
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*[[Synthetic_Biology:Press|Press]]
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*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]]
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**[http://web.media.mit.edu/~vigoda/phd/phd.htm Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing] by Ben Vigoda
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**[[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]
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*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
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===Software===
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*[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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*[http://services.alphaworks.ibm.com/manyeyes/home Many Eyes] - a site for sharing and commenting on visualizations by IBM
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*[http://simile.mit.edu/babel/ Babel] - convert between various formats (Excel, JSON, N3, RDF/XML, etc)
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*[http://iris-design.info/photoshop/web-20-style-buttons/ Web 2.0-style buttons]
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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==
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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]]

Current revision

Contact Ilya Sytchev (Илья Сычёв):

Activities

Current

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

Previous

Miscellaneous

Personal tools