Lidstrom:Back Door:Useful Links: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
| (3 intermediate revisions by the same user not shown) | |||
| Line 11: | Line 11: | ||
*[http://www.genome.jp/kegg/ KEGG] | *[http://www.genome.jp/kegg/ KEGG] | ||
*[http://metacyc.org/ Metacyc] | *[http://metacyc.org/ Metacyc] | ||
*[http://mit.edu/7.02/pdfs/nomenclature.pdf bacterial gene & knockout nomenclature] | |||
===E. coli=== | ===E. coli=== | ||
| Line 74: | Line 75: | ||
==Safety/Lab Technique== | ==Safety/Lab Technique== | ||
*[http://www.benchfly.com/video/33/working-with-sterile-technique/ Sample video]: sterile technique | *[http://www.benchfly.com/video/33/working-with-sterile-technique/ Sample video]: sterile technique | ||
== Graphics == | |||
* [http://inkscape.org/ inkscape] - SVG (vector) drawings, free. Loved by Janet & Amanda | |||
* [http://www.gimp.org/ GIMP] - pixels (like photoshp), free | |||
** [http://arstechnica.com/business/2012/05/hands-on-testing-the-gimp-28-and-its-new-single-window-interface/ website] about the interface | |||
** http://www.gimp.org/release-notes/gimp-2.8.html - shows the location plus download link | |||
==Misc== | ==Misc== | ||
Revision as of 17:56, 18 January 2013
Back to Back Door
General
- general biology/biotech basics from Integrated DNA Technologies (IDT)
- Molecular Biology Background:
- Mitochondrial DNA, Mendelian Genetics, Molecular Facts and Figures, Protein Synthesis, microRNAs, DNA Replication, A Brief History of DNA, What is an Oligo
- Molecular Biology Techniques:
- The Polymerase Chain Reaction, Gel Electrophoresis , Restriction Endonucleases , DNA Sequencing , Antisense Technologies , A Basic PCR Protocol ,
- Molecular Biology Background:
Microbiology
E. coli
- Working with E. coli
- coli Genome Stock Center
- Ecocyc
- EcoSal !!subscription required!! (not available at UW)
- origins of replication
Molecular Biology
DNA/RNA Tools
- Agarose gel electrophoresis basics
- Genewiz DNA sequencing
- IDT DNA oligos
- EBI Sequence Alignment
- BLAST! Sequence Alignment
- RBS strength calculator/engineering tool
- Accuracy stated by FAQ: "on average, the predictions of the RBS Calculator are accurate to within a factor of 2.3, equivalent to an error of 1.82 kcal/mol in the thermodynamic model. There is a 47% chance that a synthetic ribosome binding site will be accurate to within 2-fold of its predicted translation initiation rate." So you can estimate it to have accuracy within an order of magnitude. Pretty sensitive to the amount of upstream & downstream sequence info you provide. Check your forward engineering designs with more bp included in the reverse engineering mode.
- Finnzyme Tm calculator: use if you use Phusion DNA polymerase
- Finnzyme multiple primer analyzer looks for primer dimers (check before ordering primers)
- Replicons and Compatibility
- Nanodrop Info
Protein Tools
- Size Estimation
- Visualization
- Structure Prediction
- Alignment
Synthetic Biology
Mass Spec
Misc
- Mathematica (not free)
Presentations/Posters
- Website to see how colorblind people will see your slides
- University Art Pack Download: a collection of University of Washington logos
University of Washington
UW Resources
Safety/Lab Technique
- Sample video: sterile technique
Graphics
- inkscape - SVG (vector) drawings, free. Loved by Janet & Amanda
- GIMP - pixels (like photoshp), free
- website about the interface
- http://www.gimp.org/release-notes/gimp-2.8.html - shows the location plus download link
Misc
- Mendeley : reference/paper manager that's awesome
- Endy:Victor3_plate_reader/filters Filters for Fluorescence
- Equilibrator
- BioNumbers: a collection of useful bionumbers
- emolecules Chemical Lookup
