Michael Manhart, Ph.D.
Institute of Integrative Biology
8092 Zurich, Switzerland
CHN K18 (ETHZ), BU F13 (Eawag)
michael.manhart AT env.ethz.ch
+41 44 633 60 32
Research Tools and Links
Papers and preprints:
Resources for mathematics and computation:
- PubMed: search engine for journal articles in the life sciences
- arXiv: preprint server for physics, mathematics, and computer science
- bioRxiv: preprint server for biology
DNA and protein sequence analysis:
- matplotlib: amazing plotting package for Python
- 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
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:
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.
- 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.
Other web sites:
- 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.
- 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.
Professional Development for Scientists
As students we spend so much time reading textbooks or papers on science, but we spend surprisingly little time learning how to be scientists, which encompasses a lot more than just knowing science. In many ways, this kind of knowledge is at least as important to our success (and, more importantly, happiness) than the scientific knowledge itself. To this end, here is a collection of resources for scientists that I have personally found useful. This is a distinct (but not entirely mutually-exclusive) list from the above set of teaching resources, because those are supposed to be resources on scientific knowledge while this is a list of professional development tools for scientists.
- I highly recommend this classic essay in Nature from the great Steven Weinberg.
- Uri Alon, a biophysicist at the Weizmann Institute, has compiled a very nice set of resources called "Materials for Nurturing Scientists." There are lots of great articles, videos, and songs (!) here. His vision is certainly uplifting, and I highly recommend checking it out.
- Serial Mentor: Claus Wilke's (University of Texas-Austin) blog on general topics for scientists and science students.
- Ravi Vakil, a mathematician at Stanford, has some good advice on his website, especially regarding letters of recommendation (useful both for those of us asking for letters, and for those of us writing them) and the "three things" exercise for attending seminars. He has some more general advice for graduate students here.
- The mathematician John Baez (University of California-Riverside) has general advice for graduate students as well.
- The particle physicist Tommaso Dorigo (CERN) has two blog posts with several useful suggestions for graduate students (not just in particle physics, despite the post's title).
- The New York Academy of Sciences has an online resource called Science Alliance with lots of events, videos, articles, and webinars for professional development.
- Check out Joe Felsenstein's list of funding rejections ("no thanks") for his well-known phylogenetic methods. We usually just look at CVs of established scientists and are awed by all their successes; but all those successes usually lie on a background of many more rejections.
- On giving talks:
- The Tomorrow's Professor mailing list distributes lots of great articles and book excerpts on research and teaching once a week.
Last updated: 2 July 2020