It's not just bioinformatics. Wet-lab biology is often similar.
A friend of mine spent a good chunk of his PhD trying to reproduce an experiment involving growing primary cells in serum-free medium (the idea was to use that experiment as a starting point, and explore more aspects of it). The protocol was:
1. Grow some regular immortal cells in serum-based media in a dish, so they coat the dish with extracellular matrix
2. Use trypsin to detach the cells from the dish and remove them
3. Wash the dish carefully to remove all traces of serum, but leaving the extracellular matrix
4. Plate the primary cells onto the dish and grow them in serum-free medium
He tried for months and couldn't get the cells to grow. Then he got sloppy, didn't wash the dishes as carefully as he should, and bingo, the primary cells grew fine, as described in the original paper.
After some subtle digging, the inescapable conclusion was that the original authors had not washed their plates all that carefully either, and the serum-free medium was not exactly that. The whole premise of the experiment was flawed.
A friend of mine spent a good chunk of his PhD trying to reproduce an experiment involving growing primary cells in serum-free medium (the idea was to use that experiment as a starting point, and explore more aspects of it). The protocol was:
1. Grow some regular immortal cells in serum-based media in a dish, so they coat the dish with extracellular matrix
2. Use trypsin to detach the cells from the dish and remove them
3. Wash the dish carefully to remove all traces of serum, but leaving the extracellular matrix
4. Plate the primary cells onto the dish and grow them in serum-free medium
He tried for months and couldn't get the cells to grow. Then he got sloppy, didn't wash the dishes as carefully as he should, and bingo, the primary cells grew fine, as described in the original paper.
After some subtle digging, the inescapable conclusion was that the original authors had not washed their plates all that carefully either, and the serum-free medium was not exactly that. The whole premise of the experiment was flawed.