User:Ilya: Difference between revisions
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===Lab computing=== | ===Lab computing=== | ||
[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] | [[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] | ||
==Notes== | ==Notes== | ||
Revision as of 11:39, 18 January 2007
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
Semantic Web Ontology for the Registry of Standard Biological Parts.
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
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)
- 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
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