User:Ilya

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Notes)
Current revision (21:35, 28 October 2012) (view source)
 
(46 intermediate revisions not shown.)
Line 1: Line 1:
-
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].
+
__NOTOC__
 +
Contact Ilya Sytchev (Илья Сычёв):
 +
*<math>\mbox{hackdna}</math>@<math>\mbox{gmail.com}</math>
 +
*[[Special:Emailuser/Ilya|send me an email via OpenWetWare]]
-
Contact: <math>\mbox{ilyas}</math>@<math>\mbox{mit.edu}</math>
+
==Activities==
-
 
+
-
==Research==
+
===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.
===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/Win.mit.edu|WIN.MIT.EDU]]
-
===Software development===
+
*[[User:Ilya/Yeast/Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[User:Ilya/Yeast|yeast]] and [[User:Ilya/Yeast/Phylogeny|related species]]
-
[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBricks aligner] - aligns sequence reads (fragments) to Biobrick sequence
+
-
*[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
+
-
*[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Results.pm Bio::Tools::Sim4::Results] - results of one Sim4 run
+
-
*[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===
+
-
[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
+
-
 
+
-
====Data storage====
+
-
*[http://itinfo.mit.edu/article.php?id=6628 MIT TSM Backup Service]
+
-
**TSM software (free to MIT community per site license)
+
-
**Monthly service charge: $7.50 per month per computer
+
-
**TSM software is available for Windows, Mac and Linux free from [http://itinfo.mit.edu/product.php?id=7&level=all MIT]
+
-
**Backups are stored on one of the four TSM backup servers in building W91
+
-
**Manual or Scheduled Backup
+
-
**Old versions of current files and deleted files are kept for 30 days
+
-
**Need a separate account for each computer to be backed up
+
-
 
+
-
*[http://www.extremetech.com/article2/0,1697,1943502,00.asp A Tale of Two Terabyte NAS Boxes]
+
-
*[http://buffalotech.com/buffalo-home.php Buffalo Technology]
+
-
*[http://www.buffalotech.co.uk/products/category-detail.php?categoryid=29 Buffalo TeraStation Home]
+
-
**Example disk configuration: 4 x 250GB IDE (750GB in RAID5)
+
-
**Protocols: FTP, SMB
+
-
**USB 2.0 port for external hard drive (backup or additional storage)
+
-
**[http://www.pcmag.com/article2/0,1759,1780692,00.asp Review by PC Magazine]
+
-
***Bottom line: Flexible and reliable storage for everyone on your network. Print sharing is a plus, as is expandable USB disk storage.
+
-
***Pros: Offers RAID level data protection; easy-to-configure shared and private storage for all workgroup members; print sharing is a plus.
+
-
***Cons: Large footprint. No logging or reporting features.
+
-
**[http://www.extremetech.com/article2/0,1697,1917912,00.asp Review by ExtremeTech]
+
-
**[http://www.terastation.org/ TeraStation wiki]
+
-
*[http://www.buffalotech.co.uk/products/category-detail.php?categoryid=19 Buffalo TeraStation Pro]
+
-
**Released in March 2006
+
-
**S-ATA drives
+
-
*[http://www.infrant.com/products/products.php Infrant ReadyNAS]
+
-
*[http://www.infrant.com/products/products_details.php?name=ReadyNAS%20NV ReadyNAS NV]
+
-
*[http://www.infrant.com/products/products_details.php?name=ReadyNAS%20NVPlus ReadyNAS NV+]
+
-
 
+
-
==Notes==
+
-
*[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
+
-
*[http://biology-pages.info/ Kimball's Biology Pages]
+
-
*[[Bioinformatics]] @ OpenWetWare
+
-
*[[Computing/Web2.0|Web 2.0]]
+
-
*[[User:Ilya/Digital_evolution|Digital evolution]]
+
-
*[[http://web.mit.edu/network/ MIT Network and Infrastructure Team]] - network maps, etc
+
-
 
+
-
===Synthetic Biology===
+
-
*[[SB:FAQ|Synth Bio FAQ]]
+
-
*[http://www.dnahack.com/ DNA Hack] - The website for Amateur Genetic Engineering
+
-
*[[Synthetic_Biology:Press|Press]]
+
-
*using analog circuits/logic
+
-
**digital design is modular and predictable (abstraction hierarchy)
+
-
**[[Reshma_Shetty/FAQ_and_thoughts|Reshma's thoughts]]
+
-
**[http://web.media.mit.edu/~vigoda/phd/phd.htm Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing] by Ben Vigoda
+
-
**[[Wikipedia:Analog_circuit|Analog circuit]] Wikipedia article
+
-
**[http://kabuki.eecs.berkeley.edu/ Research in analog IC design]
+
-
**[http://www.falstad.com/circuit/ Circuit simulator applet]
+
-
**[http://www.circuitsage.com/ Analog design resources]
+
-
**[http://zone.ni.com/devzone/conceptd.nsf/webmain/D59654FA44D2F9FA86256F4A006064F3 Basic Analog Circuits - Tutorial]
+
-
*Cell-free synthetic biology
+
-
**[[doi:10.1126/science.1132493|Enzyme-Free Nucleic Acid Logic Circuits]], Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree
+
-
**[[doi:10.1126/science.1135101|Perspectives essay in Science: Pulling Strings]], Walter Fontana
+
-
**[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
+
-
**[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
+
-
 
+
-
===Software===
+
-
*[http://wwwhomes.uni-bielefeld.de/chase/biotool2web/ Biotool2Web]: Creating Simple Web Interfaces for Bioinformatics Applications
+
-
*[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
+
-
*[http://www.aggregatedata.com/ Aggregate Data] utilizes AJAX-based "sliders" so survey takers can choose anywhere along a spectrum of opinion
+
-
*CHM file viewers for non-Windows platforms
+
-
**[http://gnochm.sourceforge.net/ GnoCHM]
+
-
**[http://xchm.sourceforge.net/ xchm]
+
-
**[http://chmox.sourceforge.net/ Chmox] - a Mac OS X CHM viewer
+
-
*[http://tor.eff.org/ Tor]: an anonymous Internet communication system
+
-
*[http://wireshark.org/ Wireshark]: network protocol analyzer (successor to [http://www.ethereal.com/ Ethereal])
+
-
 
+
-
===Application servers===
+
-
*[http://www.whitebeam.org/ Whitebeam] - open source; applications are written as a set of XML pages that contain embedded JavaScript
+
-
[[Category:Steering Committee member]]
+
-
[[Category:People at MIT]]
+
-
 
+
-
===Miscellaneous===
+
-
*[http://www.dnaartistry.com/ DNA Art]
+
-
*[http://www.dna11.com/ DNA 11]
+
-
*[http://www.baekdal.com/web2dna/ WEB2DNA]
+
 +
==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]]

Current revision

Contact Ilya Sytchev (Илья Сычёв):

Activities

Current

Developing an integrated data management and analysis system for the Stem Cell Commons project.

Previous

Miscellaneous

Personal tools