The government might have reopened Thursday, but getting federal science agencies back into gear is still going to take some time. Backlogs have to be dealt with, offices reopened, forms processed, and boats sent out again. And for many scientists with ongoing research, lasting damage has already been done.

Research vessels were called back to shore when the shutdown began. NOAA

In this picture above, you can see the current (as of Thursday afternoon) positions of various research vessels of the National Oceanic and Atmospheric Administration – most stuck in the ports they had to hustle to when the shutdown began. While NOAA was still able to run the National Weather Service and monitor national marine sanctuaries, most ocean research activities had to be stopped. Now that those boats can put out to sea again, research can resume – but there will still be a two-week gap in their activities.

The U.S. Centers for Disease Control and Prevention had to suspend its national flu monitoring program in the midst of the shutdown. While this didn’t have much of an impact within state borders (and, luckily, struck at the very beginning of the flu season), CDC employees will now have to wade through a backlog of state data and requests for information.

During the 16-day shutdown, lab animals used by federal researchers could still receive food and water, but scientists are forbidden to work with them. This means that thousands of animals, mostly mice, will die needlessly. Some strains of lab mice are genetically altered and require special attention from scientists. Mice have also had free reign to breed while the scientists were away – and with the mouse gestation cycle lasting an average of 20 days, some laboratories may soon be overrun with new animals. Because there are strict rules about the number of mice that can be kept in cages, researchers will likely have to start culling the mice soon.

"We might start moving animals around to facilities where we have some room," Bob Adams, the director of laboratory animal medicine at Johns Hopkins University, told NPR. "But at some point we would probably have to start euthanizing animals."

Other effects won’t be immediately felt.

“Research is an iterative process, and quite often something happens that is an ‘aha’ moment,” says Georges Benjamin, executive director of the American Public Health Association, told Scientific American. “We will never know how many of those ‘aha’ moments were missed.”

For many scientists, the federal shutdown is just the latest knife in the back.

“I have 2 ongoing federal grants,” one researcher, going by the handle “99trumpets,” wrote on Reddit at the start of the shutdown. “One has already been delayed for months by sequestration, and due to that we already had to completely scrap the entire 2013 field season. (The animals are only study-able in August & September; the funding was delayed 6 [months] but you can't just go tell the animals ‘could you please postpone your breeding season till February?’”

The weeks and months ahead will provide the full tally of the damage done. Repairing the damage done to U.S. science is going to need a lot more than Vice President Joe Biden bringing muffins to the EPA.