- KiNET – a database of kinetics data and parameters of biochemical processes for E.coli. The database accumulates published data collected in the Institute of Cytology and Genetics SB RAS over seven years. KiNET presents kinetics data of biochemical reactions (conditions of experiments, values of kinetics parameters, concentrations of key metabolites, cell enzymes and other) as the web-source. Researchers from all over the world can decrease time needed for development of mathematical modeling of biochemical processes, analyzing, selecting and other tasks related with kinetics data using the KiNET database. The KiNET will be helpful in carrying out of large-scale in silico studies. Also the database can be useful as information source.
- GeneNetStudio – a software package developed for visual reconstruction and analysis of network models of molecular-genetic systems (gene networks).
**GeneNetStudio**is a new client part of GeneNet system. It provides possibilities of creating, editing and further analysis of gene networks.**GeneNetStudio**supports a system of compartments, which allow to describe the gene network based on spatial features. Software package includes such subsystems: (1) search of regulatory circuits; (2) phylogenetic decomposition of gene network; (3) conversion of associative semantic networks of molecular and genetic interactions from ANDCell system in gene networks; (4) conversion of the network models in the bipartite representation, and others. - MGSmodeller as a computer system contains the next set of modules: "model constructor/editor", "model calculation", "inverse problem", "optimal control". Multifunctionality of the system is based on the facilities of each module. Such module as "model constructor/editor" allows to create and to edit models using original standard SiBML for specification mathematical models of molecular genetic networks. The system also includes: (i) tools for model reconstruction with arbitrary structure of the molecular genetic systems taking into account positional relationship and orientation genes in genomes, polyallel genes, matrix principles of the passing such fundamental processes as replication, transcription and translation, and milticompartmental structure of studying systems, (ii) tools for dynamic calculation, solving of inverse problems and problems of optimal control. MGSmodeller is java-application and is supplied with attributes of the user friendly interfaces. User interface of the MGSmodeller allows to hierarchically represent data, edit them and to clearly represent the calculation results and to perform analysis of molecular genetic models.
- Mammoth database is designed for storage and accumulation of elementary subsystem models of biomolecular systems. Elementary subsystem model is the “functional network” model where the entities of the network and the mathematical model parameters are specified. The dynamics of each elementary subsystem model is related to published experimental data, which are referenced in the corresponding “model description” field. Each mathematical model in the database has the description field where one can find references on articles which were the basis for the model development or which contain a quantitative experimental data used for model parameters fitting. The mathematical models were manually curated and verified by expert authors. Each model in the database has been developed on basis of the general entities vocabulary. It makes possible to compare entities in the different models by identifiers directly. Using this property, MAMMOTh provides some functionality for manipulation with models. To follow the “building blocks” strategy for complex models reconstruction we have implemented a method of template models generation reconstructed by the automatic composition from a subset of elementary models which are presented in the database. These assembled models can be exported in such well known formats as SBML, MATLAB, MATHEMATICA, and Pajek for further analysis in other tools. MAMMOTh has the REST API with JSON response that available by reference: mammoth.biomodelsgroup.ru/api.
- Pajek Writer – software for generation of structural representation of biochemical processes in format Pajek on a set of the proceeding reactions presented in the form of the list of biochemical reactions.
- STEP+ -program module allows a comprehensive study of the mathematical model in the form of an autonomous system composed of n differential equations with the vector of parameters p. The STEP+ program module includes algorithms for numerical analysis of the solution of the autonomous system, depending on the model parameters: (1) multistep Gear method with a variable order of accuracy for integration of stiff systems; (2) method of solution continuation with respect to a parameter for constructing the stationary solutions diagram of the autonomous system; (3) Godunov-Bulgakov numerical criterion for determining the guaranteed asymptotic stability of stationary solutions, depending on the model parameter.
- MGSgenerator - program module generates automatically a mathematical model from the structural model of a gene network extracted from the GeneNet database (Ananko et al) and delivers it in an appropriate computer format. The model can be exported to SiBML (Likhoshvai et al., 2001), SBML (Hucka et al., 2003), and Step+ formats. The construction of a mathematical model is based on the generalized chemical-kinetic method (Likhoshvai et al., 2007) that allows describing the molecular-genetic processes linking the components of the gene network, by a nonlinear system of differential equations. The MGSgenerator matches every biological process to some template function and, based on this information, generates a mathematical model. To describe the biological processes, template models of three various levels of complexity are used that form the functions determining the right-hand sides of the system of ordinary differential equations.
- SBGN2Math - a tool for the mathematical models generation on basis of gene networks structure, reconstructed in the SBGN-PD standard. It takes the SBGN-PD file as input and generates the mathematical model in Matlab and SBML. It has the limited number of supported SBGN-PD nodes and relations.
- N_K_criterion - is the criterion for prediction of model's dynamical modes (Likhosvai et al., 2003, in Russian). This criterion can be used for gene networks with negative regulations only (where n is a nubmer of network nodes and k is a number of output arcs for each node). The criterion is implemented as Matlab tool. Moreover, the tool allows user to generate a several classes of mathematical models that can be simulated in Matlab package.