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modeling is PottersWheel (https://www.ncbi.nlm.nih.gov/pubmed/18614583). A combi­

nation of the two methods is semiquantitative modeling, whereby one is able to consider

the system state in the interval between 0 and 1, although this can be done without knowl­

edge about the kinetics. An example software is SQUAD, where the system state of a

network is first represented using a discrete system (Boolean system), identifying all

“steady state” states, which is then transformed into a dynamic system using an exponen­

tial function. Another example is Jimena (teaching software). For example, to model the

cAMP signaling pathway, one needs to assemble all the molecular components (cAMP,

receptor, signaling cascade, different cell types). From this, one can then develop a

dynamic model. This would then integrate the exact concentration levels using differential

equations (exact kinetic data required through experiments) and, for example, model either

the activity of the signalling cascade or even the drug effect in different cells as a function

of the cAMP level (e.g. with PottersWheel).

In addition to the advantages, such as rapid observation of the network behavior even

without complete experimental data, there are also disadvantages of mathematical model­

ing, such as only focused section of the living cell or intuitive observation of the network

behavior.

Question 5.16

Answer A, B, D (see also previous answers).

Question 5.17

A steady state describes the network state to which the network returns, i.e. a stable state

that is reached again even after changes/disturbances or does not change (see also previous

answers).

20.6

Extremely Fast Sequence Comparisons Identify all

the Molecules that Are Present in the Cell

Question 6.1

When I want to look something up in a book, I can either flip through the book from front

to back quickly (it’s easy to miss something). Or I look in the index, for example in this

book under “super-fast sequence comparisons“. That means I can find the right page right

away via the index. The acceleration of BLAST works the same way. Only those indices

are examined more closely (with exact alignment) that are promising. Of course, this only

works if the index is there. Creating a keyword directory for a database is called “index­

ing”, because an index (a keyword directory) is created. This has to happen with each new

version of a database (i.e. a list of sequences) before the BLAST search can then go over

the database so quickly.

20  Solutions to the Exercises