User:Ilya

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

Notes

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

WIN.MIT.EDU

Data storage

• 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 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

• A Tale of Two Terabyte NAS Boxes
• Buffalo Technology
• 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)
  • 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.
  • Review by ExtremeTech
  • TeraStation wiki
• Buffalo TeraStation Pro
  • Released in March 2006
  • S-ATA drives
• Infrant ReadyNAS
• ReadyNAS NV
• ReadyNAS NV+

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
  • GnoCHM
  • xchm
  • Chmox - a Mac OS X CHM viewer
• Tor: an anonymous Internet communication system
• Wireshark: network protocol analyzer (successor to Ethereal)

Application servers

• Whitebeam - open source; applications are written as a set of XML pages that contain embedded JavaScript

Miscellaneous

• DNA Art
• DNA 11
• WEB2DNA

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