An office. Desks, chairs, Internet, phone. Maybe even a printer. More and more, universities are providing these organizational basics to a growing number of journalism startups around the country. Offering stability, institutional prestige, and an atmosphere conducive to innovation, universities are serving as incubators for new outlets that need somewhere safe to hatch. But are these fledgling news outfits able to report the goings-on at their university nests?

There are many advantages to working within a university setting, but the arrangement raises some sticky issues about editorial independence. The line between existing within a university and dealing with a story that concerns that very institution can be difficult to navigate. As it turns out, most university-based news startups have firewalls in place to protect them from conflict-of-interest situations like that in which Diane Carman found herself.

Carman, a newspaper reporter for most of her life, is the director of communication at the School of Public Affairs at University of Colorado, Denver. She set out last year to create a news site focused on health policy, independently raising the funds to create Health Policy Solutions, a nonprofit, independent news organization housed within the School of Public Affairs. The site is funded in large part by a grant from the Colorado Health Foundation. The funding stipulated editorial independence from the school.

It launched in December 2010, with support from university administration. But soon after it started, a new chancellor was hired, and he wasn’t so enthused about the project. “His view has been that university communications should be solely for the purpose of advancing the image of the university,” says Carman. “An independent journalistic project inside the university, outside the control of the university administration, doesn’t fit that idea.”

Six weeks after launch, Solutions covered a meeting at the university’s medical school. CU Denver’s vice chancellor for health affairs wanted to tighten ethical standards around faculty members taking money from pharmaceutical companies, usually in exchange for drug talks or to consult for the companies. Some were defensive about the money they had received from drug companies, and disagreed about how far the university should go in limiting the medical staff’s ability to negotiate these contracts. Solutions wrote about the debate, and its future access to the med school was soon challenged by the medical school administration. Carman says that, after a few months of back and forth, as a gesture of “good will” she agreed to give the university a heads-up when Solutions would be covering a meeting, whenever “possible or practical.” This protected the site from missing out on last minute meetings, or ones they simply weren’t informed about.

Solutions’ independence was protected because the school had signed off on the Colorado Health Foundations grant, which had stipulated that the school would have no editorial influence over the site. She says that what they have negotiated is “an awkward relationship that allows us to continue having editorial independence, but it’s a cloud that looms over our news judgment.”

Many university-based news centers have painstakingly detailed arrangements with the schools that house them. And although Solutions’ funding is completely separate from the university, one of the main problems is that, unlike most other sites like hers, she’s in the school of Public Affairs, not a journalism school. When forming the site’s advisory board, she found herself explaining the tenets of journalistic integrity to administrators. The dean’s office described Solutions’ board members as “stakeholders,” which Carman explained would be an inappropriate name, since it implies a vested interest in how the stories are told. “This came as a stunning revelation to them,” says Carman. “It’s just one of the things that I have had to try and generate understanding around.”

Brant Houston, the former executive director of Investigative Reporters and Editors, says it’s important for any aspiring investigative site to establish itself as its own 501(c)3 nonprofit. Deriving that nonprofit status from association with the university, which is what Solutions does, does not offer as much protection. Houston is currently the Knight Chair in Investigative and Enterprise Reporting at the University of Illinois. He’s running CU-CitizenAccess, a news site that covers poverty issues in the local community. While it employs two full time reporters, the site is a part of the university, and relies on student class work for content. Though CU-CitizenAccess hasn’t yet had any administrative interference, Houston says these types of situations depend heavily on the type of reporting you are doing.

Alysia Santo is a former assistant editor at CJR.