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| [[Category:Steering Committee member]]
| | __NOTOC__ |
| [[Category:People at MIT]] | | 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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| 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].
| | ==Activities== |
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| Contact: <math>\mbox{ilyas}</math>@<math>\mbox{mit.edu}</math>
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| ==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. |
| **[[Synthetic_Biology:Semantic_web_ontology/Notes|Notes]]
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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/Spamassassin|Spamassassin]] | | **[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] |
| *[[User:Ilya/SocialNetworking| Social networking]] | | *[[User:Ilya/Yeast/Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[User:Ilya/Yeast|yeast]] and [[User:Ilya/Yeast/Phylogeny|related species]] |
| | |
| ===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 | |
| *[[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
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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===
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| *[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] | |
| *[[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://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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| ====Data visualization====
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| *[http://services.alphaworks.ibm.com/manyeyes/ Many Eyes] - a [http://many-eyes.com/ site] for sharing and commenting on visualizations by IBM
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| *[http://www.data360.co.uk/ Data360]
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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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| ===Miscellaneous===
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| *<html><a href="javascript:location.href='https://libproxy.mit.edu/cgi-bin/ezpauth?url='+location.href">MIT proxy</a></html>: 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 [http://people.csail.mit.edu/jrk/ Jonathan Ragan-Kelley])
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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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| *[http://genomequilts.com/ Genome Quilts] - a way of encoding genetic information in quilt designs
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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]] |
