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Kurihara, Akira On some examples of equations defining Shimura curves and the Mumford uniformization. J. Fac. Sci. Univ. Tokyo Sect. IA Math. 25 (1979), no. 3, 277--300.

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Reichert, Markus A. Explicit determination of nontrivial torsion structures of elliptic curves over quadratic number fields. Math. Comp. 46 (1986), no. 174, 637--658.

http://www.math.uga.edu/~pete/Reichert86.pdf

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Gonzàlez Rovira, Josep Equations of hyperelliptic modular curves. Ann. Inst. Fourier (Grenoble) 41 (1991), no. 4, 779--795.

http://www.math.uga.edu/~pete/Gonzalez.pdf

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Noam Elkies, equations for some hyperelliptic modular curves, early 1990's. [So far as I know, these have never been made publicly available, but if you want to know an equation of a modular curve, try emailing Noam Elkies!]

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Elkies, Noam D. Shimura curve computations. Algorithmic number theory (Portland, OR, 1998), 1--47, Lecture Notes in Comput. Sci., 1423, Springer, Berlin, 1998.

http://arxiv.org/abs/math/0005160

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An algorithm which was used to find explicit defining equations for $X_1(N)$, $N$ prime, can be found in

Pete L. Clark, Patrick K. Corn and the UGA VIGRE Number Theory Group, Computation On Elliptic Curves With Complex Multiplication, preprint.

http://math.uga.edu/~pete/TorsCompv6.pdf

This is just a first pass. I probably have encountered something like 10 more papers on this subject, and I wasn't familiar with some of the papers that others have mentioned.

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No, there does not exist a comprehensive list of equations: the known equations are spread out over several papers, and some people (e.g. Noam Elkies, John Voight; and even me) know equations which have not been published anywhere.

When I have more time, I will give bibliographic data for some of the papers which give lists of some of these equations. Some names of the relevant authors: Ogg, Elkies, Gonzalez, Reichert.

In my opinion, it would be a very worthy service to the number theory community to create an electronic source for information on modular curves (including Shimura curves) of low genus, including genus formulas, gonality, automorphism groups, explicit defining equations...In my absolutely expert opinion (that is, I make and use such computations in my own work, but am not an especially good computational number theorist: i.e., even I can do these calculations, so I know they're not so hard), this is a doable and even rather modest project compared to some related things that are already out there, e.g. William Stein's modular forms databases and John Voight's quaternion algebra packages.

It is possible that it is a little too easy for our own good, i.e., there is the sense that you should just do it yourself. But I think that by current standards of what should be communal mathematical knowledge, this is a big waste of a lot of people's time. E.g., by coincidence I just spoke to one of my students, J. Stankewicz, who has spent some time implementing software to enumerate all full Atkin-Lehner quotients of semistable Shimura curves (over Q) with bounded genus. I assigned him this little project on the grounds that it would be nice to have such information, and I think he's learned something from it, but the truth is that there are people who probably already have code to do exactly this and I sort of regret that he's spent so much time reinventing this particular wheel. (Yes, he reads MO, and yes, this is sort of an apology on my behalf.)

Maybe this is a good topic for the coming SAGE days at MSRI?