Mathematics
Proof
On Proof and Progress in Mathematics, William Thurston
Problems
Problems on Mapping Class Groups and Related Topics, Benson Farb, ed.
Questions in Geometric Group Theory, Mladen Bestvina
Problems in Geometric Group Theory Wiki
Problems in Low-dimensional Topology, Rob Kirby
Problems In Groups, Geometry, and Three-Manifolds, Kelly Delp, Diane Hoffoss, and Jason Fox Manning
Problems In Foliations and Laminations of 3-Manifolds, Danny Calegari
Problems on Boundaries of Groups and Kleinian Groups, Misha Kapovich
Blogs
Low Dimensional Topology
Geometry and the Imagination, Danny Calegari
Quomodocumque, Jordan Ellenberg
Software
SAGE example: Fibonacci numbers, Vince Lucarelli
SAGE example: Enumerating graphs, Vince Lucarelli
SnapPea, Jeffrey Weeks
SnapPy, Marc Culler, Nathan Dunfield, et. al.
KnotInfo
Knot Plot
XTrain, Peter Brinkmann
Trains and Dynn, Toby Hall
Danny Calegari's software
---The CompuTop.org Software Archive
Books
A List of Recommended Books in Topology, Allen Hatcher
Books for Graduate Students in Topology, Dan Margalit
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