PMC:4342829 / 6748-7629 JSONTXT

{"project":"2_test","denotations":[{"id":"25880925-17590932-14893496","span":{"begin":622,"end":624},"obj":"17590932"},{"id":"25880925-20212527-14893497","span":{"begin":625,"end":627},"obj":"20212527"},{"id":"25880925-22871648-14893498","span":{"begin":797,"end":799},"obj":"22871648"},{"id":"25880925-15254541-14893499","span":{"begin":874,"end":876},"obj":"15254541"}],"text":"Despite these contributions, there is still a lack of suitable benchmark problems in systems biology that are at the same time (i) dynamic, (ii) large-scale, (iii) ready-to-run, and (iv) available in several common formats. None of the above mentioned collections possesses all these features, although each one has a subset of them. Here we present a collection of medium and large-scale dynamic systems, with sizes of tens to hundreds of variables and hundreds to thousands of estimated parameters, which can be used as benchmarks for reverse-engineering techniques. The collection includes two Escherichia coli models [23,24], a genome-wide kinetic model of Saccharomyces cerevisiae [25], a metabolic model of Chinese Hamster Ovary (CHO) cells [26], a signal transduction model of human cells [27], and a developmental gene regulatory network of Drosophila melanogaster [28-30]."}