DNA
Computing @ decal's security shed
PCR
Science@NASA
Headline News
>
2002
>
Voyage of the Nano-Surgeons
Gear
OpenPCR
Chai Biotechnologies Inc. ©
:
vendor of an open source dual channel real-time
PCR
thermalcycler
OpenPCR in Nature Magazine
MiniPCR DNA Discovery System™
Software
oligdna.c
-
console mode oligonucleotide sequence generator I wrote
RDML
:
Real-time PCR Data Markup Language
Dynamic Programming, the Needleman/Wunsch DNA global sequence alignment technique
NeoBio: Bioinformatics Algorithms in Java
Jmol: an open-source browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D
Sequence Manipulation Suite at
bioinformatics.org
Academic/Research Material
DNA Computing Lecture Notes
Web Index of my
DNAC
Professor (David Harlan Wood)
Basic DNA Computing
Molecular Bioinformatics 2001, Uppsala University
-
Lecture Notes by Per Kraulis
Algorithms for Computational Molecular Biology
Circuits, Computation and Biology at the University of Minnesota's Department of Computer and Electrical Engineering
Development of a micro PCR reactor for Lab-on-Chip devices
BioBricks Foundation
Real-Time PCR Technology Basics
Transcription, Translation and Replication
Microsoft Research
:
Programming DNA Circuits (SilverLight and
OCaml
)
General Purpose Parallel Computation on a
DNA
Substrate
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
molecular-programming.org
Social Networking
Forums, MeetUps, Hacker Spaces, etc.
Biohack.me
Forum
ResearchPeptides.com
Forum
Biocurious - Silicon Valley's Hackerspace for Biotech
BIOLOGIK LABS - Community BioHackerSpace in Virginia
StartUps
Pearl BioTech: Tito Jankowski's Company (Co-inventor of OpenPCR)
editas medicine: CRISPR Cas9 Start-up in Cambridge
CRISPR Therapeutics: Gene Editing Company Focused on Development of Transformative Medicines
The ODIN: Kits and Tools for Consumer Genetic Design
Miscellaneous
Beyond Genetics: DNA in Nanotechnology
Programming DNA Circuits at Microsoft Research
Visual
DSD
Silverlight Applet Manual
DNA Computing Verification
The international
SAT
Competitions web page
HTML Books on the History of Evolutionary Biology (from Aristotle to Mendel's Rediscovery)
BioJava Wiki Pages
Haploview Screenshots
Outline on Basic DNA Lab Technology for DNA Computing
Structure and physiological properties of DNA
Ligation - joining two separate strands together to form one long strand a.k.a. 'elongation'
Annealing - when two complementary strands wrap around each other to form a double helix
Hybridization - two non-complementary strands bind only where nucleic acid sequences are favorable
Denaturation - causes bound strands to melt away from each other and become individuals
"
Duplex
DNA" has alternative double-helical structures; B, A and Z-forms
"
Closed
DNA" (a single strand with both ends joined together) twists upon itself & forms a 'supercoil'
Important enzymes relevant to DNA Computing
Restriction Endonuclease
Taq Polymerase
P
fu
DNA Polymerase
Essential Laboratory techniques relevant to DNA Computing
AGE
(Agarose Gel Electrophoresis) separates DNA by length via electro-osmotic flow
DNA Sequencing Techniques
qPCR (Real-Time Polymerase Chain Reaction)
DNA Cloning
DNA Amplification
DNA Purification
