The score is calculated in three parts.
1) The reputation score is a count of the number of followers you have.
2) The contribution score takes into account the number of repositories you have. It factors in the number of watchers for each repository as well as the number of forks. It then doubles that score if you are the original owner of the repository (rather than the repository being a fork itself).
3) The gist score takes into account the number of gists you have as well as the comments on those gists.