Lidstrom:Back Door:Useful Links: Difference between revisions
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**[http://www.pymol.org/ Pymol] | **[http://www.pymol.org/ Pymol] | ||
** tutorial: [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners] | ** tutorial: [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners] | ||
* tutorial: [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf bioquest.org] | ** tutorial: [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf bioquest.org]. Concise less basic review | ||
** tips/examples: [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips] | ** tips/examples: [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips] | ||
** tutorial: [http://www.doe-mbi.ucla.edu/CHEM125/pymol_tutorial_060418.pdf UCLA] | |||
**[http://www.cgl.ucsf.edu/chimera/download.html Chimera] | **[http://www.cgl.ucsf.edu/chimera/download.html Chimera] | ||
*Structure Prediction | *Structure Prediction | ||
Revision as of 05:49, 1 October 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:
- Qiagen Bench Guide
- cell culture & DNA
Microbiology
E. coli
- Working with E. coli
- coli Genome Stock Center
- Ecocyc
- EcoSal !!subscription required!! (not available at UW)
- origins of replication
- RegulonDB A curated database of E. coli regulation.
Molecular Biology
DNA/RNA Tools
plasmid annotations
- APE free plasmid editor
- Serial Cloner free equivalent to Vector NTI
- PlasMapper
- The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format.
other
- Agarose gel electrophoresis basics
- Genewiz DNA sequencing
- IDT DNA oligos
- EBI Sequence Alignment
- BLAST! Sequence Alignment
- The most commonly used nucleotide/protein alignment tool.
- start here (animated web intro)
- Practical intro: CHS protocols
- RBS strength calculator/engineering tool
- Another: link
- 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
- NuPack Nucleic acid secondary structure predictor
BioBricks
Protein Tools
- Size Estimation
- Visualization
- Pymol
- tutorial: pymol for beginners
- tutorial: bioquest.org. Concise less basic review
- tips/examples: figure tips
- tutorial: UCLA
- Chimera
- Structure Prediction
- Alignment
Enzymes
Synthetic Biology
Mass Spec
HPLC
- Shimadzu Virtual Advisor.
- Ask Nicole, Amanda, or Janet for the lab log-in.
Programming/Scripting
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
- Inkscape: Guide to a Vector Drawing use examples
- 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
- drawing chemical structures: (ask Amanda about either of these)
- chemsketch (free)
- chemdraw (seems to cost $)
Misc
- Mendeley : reference/paper manager that's awesome
- Janet's workflow: (1) discover papers via google scholar saved search, (2) save them to Mendeley in the appropriate nested folder regardless of whether you intend to read it now or "some day when I'm thinking about that topic" (3) read in Mendeley, which makes a green dot (indicating unread) go away.
- You can highlight and keep notes on top of your PDFs enabling quicker review of topics.
- Imagine being able to query all of the papers you have ever read for a topic of interest! You can also see whether you have ever read a paper or not, potentially saving yourself time.
- I also like the idea that I will never lose track of a paper I want to tell someone about. It isn't uncommon for someone to tell me about a paper but be unable to find it and send it to me. This should never happen for a dedicated Mendeley user.
- Endy:Victor3_plate_reader/filters Filters for Fluorescence
- Equilibrator
- BioNumbers: a collection of useful bionumbers
- emolecules Chemical Lookup
