User:Ilya
Ilya Sytchev (Илья Сычёв) is a graduate student in Bioinformatics at Northeastern University working in Endy Lab at MIT.
Contact: [math]\displaystyle{ \mbox{ilyas} }[/math]@[math]\displaystyle{ \mbox{mit.edu} }[/math]
Research
Current
Previous
Mating pheromone response pathway analysis across yeast and related species
Activities
OpenWetWare
Software development
BioBricks aligner - aligns sequence reads (fragments) to Biobrick sequence
- Sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
- A computer program for aligning a cDNA sequence with a genomic DNA sequence (backup link)
- Bio::Tools::Run::Alignment::Sim4 - wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
- Bio::SearchIO::sim4 - parser for Sim4 alignments
- Bio::Tools::Sim4::Exon - a single exon determined by an alignment
- Bio::Tools::Sim4::Results - results of one Sim4 run
- Sim4.pm - CVS log (latest version)
Lab computing
Notes
- DNA seen through the eyes of a coder
- Kimball's Biology Pages
- Bioinformatics @ OpenWetWare
- Web 2.0
- Digital evolution
- MIT Network and Infrastructure Team - network maps, etc
- IAP
Synthetic Biology
- Synth Bio FAQ
- DNA Hack - The website for Amateur Genetic Engineering
- Press
- using analog circuits/logic
- digital design is modular and predictable (abstraction hierarchy)
- Reshma's thoughts
- Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing by Ben Vigoda
- Analog circuit Wikipedia article
- Research in analog IC design
- Circuit simulator applet
- Analog design resources
- Basic Analog Circuits - Tutorial
- Cell-free synthetic biology
- Enzyme-Free Nucleic Acid Logic Circuits, Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree
- Perspectives essay in Science: Pulling Strings, Walter Fontana
- Construction of an in vitro bistable circuit from synthetic transcriptional switches, Jongmin Kim, Kristin S White and Erik Winfree
- Cell-free synthetic biology: a bottom-up approach to discovery by design, Michael L Simpson
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
- <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 Jonathan Ragan-Kelley)
- DNA Art
- DNA 11
- WEB2DNA
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