Computational topology

Algorithmic topology, or computational topology, is a subfield of topology with an overlap with areas of computer science, in particular, computational geometry and computational complexity theory.
A primary concern of algorithmic topology, as its name suggests, is to develop efficient algorithms for solving problems that arise naturally in fields such as computational geometry, graphics, robotics, structural biology and chemistry, using methods from computable topology.
Major algorithms by subject area.
Algorithmic 3-manifold theory.
A large family of algorithms concerning 3-manifolds revolve around normal surface theory, which is a phrase that encompasses several techniques to turn problems in 3-manifold theory into integer linear programming problems.
At present the JSJ decomposition has not been implemented algorithmically in computer software. Neither has the compression-body decomposition. There are some very popular and successful heuristics, such as SnapPea which has much success computing approximate hyperbolic structures on triangulated 3-manifolds. It is known that the full classification of 3-manifolds can be done algorithmically.
Computational homology.
Computation of homology groups of cell complexes reduces to bringing the boundary matrices into Smith normal form. Although this is a completely solved problem algorithmically, there are various technical obstacles to efficient computation for large complexes. There are two central obstacles. Firstly, the basic Smith form algorithm has cubic complexity in the size of the matrix involved since it uses row and column operations which makes it unsuitable for large cell complexes. Secondly, the intermediate matrices which result from the application of the Smith form algorithm get filled-in even if one starts and ends with sparse matrices.