Monitoring the reprogramming process. Green and red nodes/links represent wild type and reprogramming paths, respectively. States in the cell cycle biological path are colored in blue. States on the reprogramming path from the wild type attractor to the reprogrammed attractor are colored in pink. Cell cycle, sporulation and other attractors are colored in blue, red and black respectively. The width of the links is proportional to the transition flux. For the clarity of illustration, we only (A) plot 320 transitions between 254 states selected from 9213 transitions between 7191 states in the reprogramming from cell cycle to sporulation under the growth condition by the recipe of GCN5OERDP3KDSUM1KDTUP1KD, (B) plot 350 transitions between 255 states selected from 14157 transitions between 11089 states in the reprogramming from sporulation to cell cycle under the sporulation condition by the recipe of IME1KDMIG1OEMSN4KDTUP1OE. (C) Example of reprogramming paths from the cell cycle attractors to the sporulation attractors under the growth condition. C1 and C2 are two different cell cycle attractors and S is a sporulation attractor. Each node represents a state on the reprogramming paths and the height reflects the potential in the landscape. See also Additional file 5, Table S5.