Spending three hours a day on the South Shore Line would make anyone depressed!

I bet you can get a software internship gig near you. Contact professors doing computational work at Notre Dame (http://ibms.nd.edu/clusters/computational-biology-bioinforma...) they may have room in their budget. Though the pay will not be extravagant.

Indeed shows 300+ software gigs in South Bend: http://www.indeed.com/jobs?q=software&l=South+Bend%2C+IN

But DELETE THE FUCKING ARTICLE man. Obviously, it isn't helping your cause.

Also definitely sue your former employer: https://news.ycombinator.com/item?id=8597953