User:Ilya/Notes

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(New page: ==Synthetic Biology== *Synth Bio FAQ *[http://www.dnahack.com/ DNA Hack] - The website for Amateur Genetic Engineering *Press *using analog circuits/...)
Current revision (16:43, 2 January 2008) (view source)
 
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==Synthetic Biology==
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*[[User:Ilya/Notes/Synthetic_Biology|Synthetic Biology]]
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*[[SB:FAQ|Synth Bio FAQ]]
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*[[User:Ilya/Notes/Software|Software]]
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*[http://www.dnahack.com/ DNA Hack] - The website for Amateur Genetic Engineering
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*[[User:Ilya/Notes/Digital_evolution|Digital evolution]]
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*[[Synthetic_Biology:Press|Press]]
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*[[User:Ilya/Notes/IAP2007|IAP2007]]
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*using analog circuits/logic
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*[[User:Ilya/Notes/IAP2008|IAP2008]]
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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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*[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
*[[Bioinformatics]] @ OpenWetWare
*[[Computing/Web2.0|Web 2.0]]
*[[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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*[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
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*[[User:Ilya/IAP|IAP]]
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*[http://biology-pages.info/ Kimball's Biology Pages]
*<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])
*<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])
*[http://www.dnaartistry.com/ DNA Art]
*[http://www.dnaartistry.com/ DNA Art]
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*[http://genomequilts.com/ Genome Quilts] - a way of encoding genetic information in quilt designs
*[http://genomequilts.com/ Genome Quilts] - a way of encoding genetic information in quilt designs
*[http://fooplot.com/ FooPlot] - online graphing calculator
*[http://fooplot.com/ FooPlot] - online graphing calculator
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*[http://molecularmovies.org/ Molecular Movies] - a portal to cell and molecular animation

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