Resources

Research Tools and Links

Papers and preprints:

§ PubMed: search engine for journal articles in the life sciences

§ arXiv: preprint server for physics, mathematics, and computer science

§ bioRxiv: preprint server for biology

Databases:

§ BioNumbers: database of important numbers in biology

§ Protein Data Bank: database of protein structures

§ ProTherm and ProNIT: databases of protein biophysics and protein-DNA interactions

§ BioGRID: database of biological interactions

§ Gene Ontology: database of gene classifications

§ GenBank: NIH database of genetic sequences

§ Saccharomyces Genome Database: database of yeast genomics

§ EcoCyc: database of E. coli

§ FlyBase: database of fruit fly (Drosophila) genomics

§ DBAASP:  database of Antimicrobial Activity and Structure of Peptides  

§  NDARO: National Database of Antibiotic Resistant Organisms 

§ CARD: The Comprehensive Antibiotic Resistance Database

§ HMDB: Human Metabolome Database

§ KINOME: Kinase database

Resources for mathematics and computation:

§ matplotlib: amazing plotting package for Python

§ D3: cool visualization tools in JavaScript

§ Wolfram MathWorld: encyclopedia of mathematics

§ Wolfram Alpha: knowledge engine of science and mathematics

§ Sage: open-source mathematics software (Python-based) to rival Mathematica and Maple

§ OEIS: Online Encyclopedia of Integer Sequences

DNA and protein sequence analysis:

§ BioStar and SEQanswers: forums for sequencing and sequence analysis

§ Bowtie and Bowtie 2: short-read alignment software

§ BWA: short-read alignment software

§ SAMtools and Picard: tools for processing Sequence Alignment/Map (SAM) files

§ Genome Analysis Toolkit (GATK): suite of tools from the Broad Institute for analyzing short-read sequencing data

§ FreeBayes and VarScan: variant detection

§ ProbCons and Clustal: multiple sequence alignment

§ PHYLIP: phylogenetic inference package

§ ART: simulated high-throughput sequencing data

§ breseq: analysis pipeline for high-throughput sequencing data from microbial evolution experiments

Teaching Resources

Educational games. Games are emerging as a promising new method of teaching science, supported by a growing body of education research. I think physics lends itself particularly well to games — many physics phenomena are highly dynamic and a bit removed from our everyday experiences (think quantum mechanics and relativity), making the visual and interactive simulations offered by games incredibly useful for developing intuition. Here are some links to interesting games I've found:

§ PhETs: These are educational simulators, from the renowned physics education research group at the University of Colorado-Boulder, on various topics in science and mathematics. See also their research page for relevant citations on using them in courses.

§ Foldit: A game and visualization tool (not a simulator) for folding and designing protein molecules from David Baker's group at the University of Washington.

§ EteRNA: Similar to Foldit, but for designing RNA molecules.

§ Minecraft: Not exactly an educational game, Minecraft is nevertheless an amazing game with a strong flavor of engineering and problem-solving. There are also many cool extensions, such as the quantum mechanics-inspired qCraft.

§ A Slower Speed of Light: A simple game from the MIT Game Lab that simulates a world with a much slower speed of light, making ordinary motions highly relativistic. It's an amazing way to gain intuition for the predictions of special relativity.

§ Spin Glasses: This is a board game based on the concept of a spin glass. It seems like a potentially cool way to teach concepts such as magnetism, entropy, temperature, phase transitions, and frustration.

§ ScienceGameCenter: A site with many more science-based games.

Science blogs. Blogs are also an emerging force in science education and communication (see above for my modest efforts in this area). Here is a (very) small sample of some good science blogs.

§ Empirical Zeal (Wired Magazine) (original site): Outstanding blog by Aatish Bhatia, a former colleague of mine at Rutgers, on all sorts of topics in science and engineering.

§ Preposterous Universe: Blog by Sean Carroll (Caltech) on many topics in science and philosophy, but especially particle physics and cosmology.

§ Of Particular Significance: Matt Strassler's encyclopedic blog on particle physics, especially oriented toward research at CERN and the LHC.

§ Telliamed Revisited: Blog by Richard Lenski (Michigan State University) on evolutionary biology, especially his famous long-term evolution experiment with E. coli.

§ A Quantum Diaries Survivor: Blog by Tommaso Dorigo (CERN) on particle physics and occasionally more general topics in science.

§ Dynamic Ecology: A group blog focused on ecology and evolution.

§ Phenomena from National Geographic: A collection of professional blogs on many topics from renowned science writers.

§ Scientific American Blogs: Science blogs on lots of topics from professional scientists and science writers.

§ PLOS Blogs: From the Public Library of Science (PLOS) family of journals, mostly blogs for professional scientists rather than the general public.

Other web sites:

§ Understanding Evolution: A fantastic collection of educational resources for all things evolution, from the University of California-Berkeley.

Keith's Think Zone: A nice set of intuitive explanations for many concepts in basic math.