SBMLmerge, a System for Combining Biochemical Network Models

The Systems Biology Markup Language (SBML) is an XML-based format for representing mathematical models of biochemical reaction networks, and it is likely to become a main standard in the systems biology community. As published mathematical models in cell biology are growing in number and size, modular modelling approaches will gain additional importance. The main issue to be addressed in computer-assisted model combination is the specification and handling of model semantics. The software SBMLmerge assists the user in combining models of biological subsystems to larger biochemical networks. First, the program helps the user in annotating all model elements with unique identifiers pointing to databases such as KEGG or Gene Ontology. Second, during merging, SBMLmerge detects and resolves various syntactic and semantic problems. Typical problems are conflicting variable names, elements which appear in more than one input model, and mathematical problems arising from the combination of equations. If the input models make contradicting statements about a biochemical quantity, the user is asked to choose between them. In the end the merging process results in a new, valid SBML model

Changes in Myosin and Myosin Light Chain Kinase During Myogenesis

Myosins and myosin light chain kinases have been isolated from a cloned line of myoblasts (L5/A10) as this cell line undergoes differentiation toward adult muscle. At least three myosin isozymes were obtained during this developmental process. Initially a nonmuscle type of myosin was found in the myoblasts. The molecular weights of the myoblast light chains were 20 000 and 15 000. Myosin isolated from early myotubes had light chains with molecular weights of 20 000 and 19 500. Myosin isolated from myotubes which contained sarcomeres had light chains with molecular weights of 23 000, 18 500, and 16000. This last myosin was similar in light chain complement to adult rat thigh muscle. Two forms of the myosin light chain kinase activity were detected: a calciumindependent kinase in the myoblasts and a calcium-dependent kinase in the myotubes with sarcomeres. No myosin light chain kinase activity was detected in the early myotubes

Changes in Myosin and Myosin Light Chain Kinase During Myogenesis

Myosins and myosin light chain kinases have been isolated from a cloned line of myoblasts (L5/A10) as this cell line undergoes differentiation toward adult muscle. At least three myosin isozymes were obtained during this developmental process. Initially a nonmuscle type of myosin was found in the myoblasts. The molecular weights of the myoblast light chains were 20 000 and 15 000. Myosin isolated from early myotubes had light chains with molecular weights of 20 000 and 19 500. Myosin isolated from myotubes which contained sarcomeres had light chains with molecular weights of 23 000, 18 500, and 16000. This last myosin was similar in light chain complement to adult rat thigh muscle. Two forms of the myosin light chain kinase activity were detected: a calciumindependent kinase in the myoblasts and a calcium-dependent kinase in the myotubes with sarcomeres. No myosin light chain kinase activity was detected in the early myotubes

Toward community standards and software for whole-cell modeling

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. Results: Our analysis revealed several challenges to representing WC models using the current standards. Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance:We anticipate that these new standards and software will enable more comprehensive models

On Chemical Reaction Network Design by a Nested Evolution Algorithm

International audienceOne goal of synthetic biology is to implement useful functions with biochemical reactions, either by reprogramming living cells or programming artificial vesicles. In this perspective, we consider Chemical Reaction Networks (CRN) as a programming language, and investigate the CRN program synthesis problem. Recent work has shown that CRN interpreted by differential equations are Turing-complete and can be seen as analog computers where the molecular concentrations play the role of information carriers. Any real function that is computable by a Turing machine in arbitrary precision can thus be computed by a CRN over a finite set of molecular species. The proof of this result gives a numerical method to generate a finite CRN for implementing a real function presented as the solution of a Polynomial Initial Values Problem (PIVP). In this paper, we study an alternative method based on artificial evolution to build a CRN that approximates a real function given on finite sets of input values. We present a nested search algorithm that evolves the structure of the CRN and optimizes the kinetic parameters at each generation. We evaluate this algorithm on the Heaviside and Cosine functions both as functions of time and functions of input molecular species. We then compare the CRN obtained by artificial evolution both to the CRN generated by the numerical method from a PIVP definition of the function, and to the natural CRN found in the BioModels repository for switches and oscillators