User:Ilya/Notes
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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
- 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
- <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
- Genome Quilts - a way of encoding genetic information in quilt designs
- FooPlot - online graphing calculator
