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BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cell, virtual physiological human and virtual patient. BioUML spans a comprehensive range of capabilities, including access to biological databases, powerful tools for systems biology (visual modelling, simulation, parameters fitting and analyses), a genome browser, scripting (R, JavaScript) and a workflow engine. Due to integration with the Galaxy platform and R/Bioconductor, BioUML provides powerful possibilities for the analyses of omics data. The plug-in-based architecture allows the user to add new functionalities using plug-ins. To facilitate a user focus on a particular task or database, we have developed several predefined perspectives that display only those web interface elements that are needed for a specific task. To support collaborative work on scientific projects, there is a central authentication and authorization system (https://bio-store.org). The diagram editor enables several remote users to simultaneously edit diagrams.

Transition metal oxides are attractive noble metal-free catalysts of the oxygen reduction for application at the cathode of alkaline membrane fuel cells or metal-air batteries. However, despite of a rapidly increasing number of publications devoted to the oxygen electrocatalysis on transition metal oxides, a clear picture regarding the relations between their structure and composition on the one hand and electrocatalytic activity on the other hand is lacking. This short review discusses challenges facing researchers seeking to understand electrocatalysis of the oxygen reduction reaction on transition metal oxides.

Understanding the basic mechanisms of transcription regulation is a major challenge in modern biology. Regulation of transcription is a complex process in which transcription factors (TFs) play a key role. Chromatin immunoprecipitation followed by high throughput sequencing is a widely and intensively used experimental technology for the identification of TF binding sites (TFBSs). Nowadays, there are tens or hundreds of ChIP-seq datasets measured for the same transcription factor. Meta-processing of such datasets into an integrated dataset is relevant. We have developed a novel method for creating these integrated datasets of TFBSs. This method consists of a three-stage application of the Rank Aggregation approach. The identified TFBSs can be sorted to further select the most reliable TFBSs. We have found a high saturation of site motifs in the most reliable TFBSs. We have also demonstrated that the most reliable TFBSs prefer to be located in open chromatin regions.

Manganese oxides are known as active catalysts for the oxygen reduction reaction (ORR) in alkaline media. Being poor electronic conductors, for electrochemical applications, most of Mn oxides are either mixed with or supported on carbon materials, which impart electronic conductivity to the composite electrodes. A number of recent publications reported an immense influence of carbon materials on the electrocatalytic activity of transition metal oxides in the ORR. To better understand the role of carbon, in this work we utilize a wide variety of carbon materials and investigate the ORR on Mn 2 O 3 /carbon composites combining experiment with kinetic modeling. Such an approach allows us to discriminate the contribution of carbon in the ORR activity of composites, underscoring its positive role in improving the oxide utilization, and acting as the ORR co-catalyst, but also its negative role in competing for the adsorption of O 2 . By juxtaposing the electrocatalytic activity with the structural and morphological characteristics carbon materials, we propose some rules of thumb for choosing carbons necessary for creating efficient oxide/carbon ORR electrocatalysts.

We consider compositional and structural factors which can affect the activity of bixbyite α-Mn2O3 towards the oxygen reduction reaction (ORR) and the stability of this oxide in alkaline solution. We compare electrochemistry of undoped, Fe and Al-doped α-Mn2O3 with bixbyite structure and braunite Mn7SiO12 having bixbyite-related crystal structure, using the rotating disk electrode (RDE), the rotating ring-disk electrode (RRDE), and cyclic voltammetry (CV) techniques. All manganese oxides under study are stable in the potential range between the ORR onset and ca. 0.7 V vs. Reversible Hydrogen Electrode (RHE). It is found that any changes introduced in the bixbyite structure and/or composition of α-Mn2O3 lead to an activity drop in both the oxygen reduction and hydrogen peroxide reactions in this potential interval. For the hydrogen peroxide reduction reaction these modifications also result in a change in the nature of the rate-determining step. The obtained results confirm that due to its unique crystalline structure undoped α-Mn2O3 is the most ORR active (among currently available) Mn oxide catalyst and favor the assumption of the key role of the (111) surface of α-Mn2O3 in the very high activity of this material towards the ORR.

Hydrogen peroxide has been detected as a reaction intermediate in the electrochemical oxygen reduction reaction (ORR) on transition-metal oxides and other electrode materials. In this work, we studied the electrocatalytic and catalytic reactions of hydrogen peroxide on a set of Mn oxides, Mn2O3, MnOOH, LaMnO3, MnO2, and Mn3O4, that adopt different crystal structures to shed light on the mechanism of the ORR on these materials. We then combined experiment with kinetic modeling with the objective to correlate the differences in the ORR activity to the kinetics of the elementary reaction steps, and we uncovered the importance of structural and compositional factors in the catalytic activity of the Mn oxides. We concluded that the exceptional activity of Mn2O3 in the ORR is due to its high catalytic activity both in the reduction of oxygen to hydrogen peroxide and in the decomposition of the latter, and furthermore, we proposed a tentative link between crystal structure and reactivity.

Creating a complete picture of the regulation of transcription seems to be an urgent task of modern biology. Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins. Over the past decade, ChIP-Seq has become the most common experimental technology studying genome-wide interactions between TFs and DNA. We assessed the transcriptional significance of cell line-specific features using regression analysis of ChIP-Seq datasets from the GTRD database and transcriptional start site (TSS) activities from the FANTOM5 expression atlas. For this purpose, we initially generated a large number of features that were defined as the presence or absence of TFs in different promoter regions around TSSs. Using feature selection and regression analysis, we identified sets of the most important TFs that affect expression activity of TSSs in human cell lines such as HepG2, K562 and HEK293. We demonstrated that some TFs can be classified as repressors and activators depending on their location relative to TSS.

Knowledge on the mechanisms of oxygen reduction reaction (ORR) and descriptors linking the catalytic activity to the structural and electronic properties of transition metal oxides enable rational design of more efficient catalysts. In this work ORR electrocatalysis was studied on a set of single and complex Mn (III) oxides with a rotating disc electrode method and cyclic voltammetry. We discovered an exponential increase of the specific electrocatalytic activity with the potential of the surface Mn(IV)/Mn(III) red-ox couple, suggesting the latter as a new descriptor for the ORR electrocatalysis. The observed dependence is rationalized using a simple mean-field kinetic model considering availability of the Mn( III) centers and adsorbate-adsorbate interactions. We demonstrate an unprecedented activity of Mn2O3, ca. 40 times exceeding that of MnOOH and correlate the catalytic activity of Mn oxides to their crystal structure. (C) 2015 Elsevier Ltd. All rights reserved.

Recently, while studying the oxygen reduction reaction (ORR) in alkaline medium on Mn oxides with various crystal structures, we documented [1] an unparalleled activity of Mn2O3 oxide with bixbyite structure. Then we also observed a clear correlation of the electrocatalytic activity with the formal potential of Mn(IV/III) interfacial redox transition and suggested the ORR mechanism involving this transition as a mediator step. To extend our understanding of this complex mechanism, we also compared the behavior of various oxides in peroxide oxidation/reduction reactions [2] and in respect to the peroxide yield during the ORR. All materials were studied in the form of composites with Sibunit carbon (weight ratio 1:1). This carbon binder provides a high utilization of the oxide surface in electrocatalysis [3]. The voltammetry in deairated 1M NaOH solution and rotating disc electrode (RDE) measurements in the same but O2-saturated solution were used to determine the total charge and the ORR kinetic currents. Rotating ring disc electrode (RRDE) was applied to compare the peroxide yields on various Mn oxides. All the values were compared after normalizing them to the BET surface area. The number of electrons involved in the oxygen reduction was close to 4 and 3 for more and less active oxides, respectively. Less active oxides demonstrated significantly higher peroxide yields and slower peroxide reduction, with a convection-independent limiting current which documents a slow chemical step in a wide potential region. The independent experimental facts which can be considered for comparison with simulations are as follows: surface concentration of the Mn active centers (estimated from the total charge in Mn(IV/III) transition region); specific activity of pure carbon generating additional peroxide, which further reacts on the oxide component in carbon-oxide composites (see in Ref.[4] about the dual role of carbon); ORR polarization curves; polarization curves for peroxide reactions; peroxide yield during the ORR. This wide set of data provides a valuable input for multi-parametric simulations, which significantly decreases the number of possible solutions. The modeling involved the rate constants for five reaction steps as well as the parameter for interactions of the adsorbed oxygen species involved in the Mn(IV/III) transition (in terms of Frumkin isotherm). We found that the complete set of data can be interpreted only assuming the structural dependence of at least two rate constants: one at the initial stage (peroxide formation) and another at the final stage (peroxide reduction). Another intriguing possibility to explain the very high Mn2O3 activity in the ORR is to assume a direct ORR pathway for this oxide, and to consider a series pathway for all other oxides. To elucidate whether the latter hypothesis is reasonable, we addressed the O-O bond break on Mn2O3 and MnOOH (typical examples of high and low activities, respectively) in the framework of a quantum chemical approach resting on the cluster model of the oxide surface and the DFT level of theory. The computational results were used to map the effective reaction path. We found that for both model surfaces the direct bond cleavage at the oxide surface is hardly feasable both for the O2 molecule and most likely for peroxide intermediates. This finding makes it possible to exclude the direct pathway and to focus on molecular reasons of the structural effects on the rate constant for other steps such as the reduction of the adsorbed peroxide intermediate. The work is supported by EraNetRus program, project (#270 NANO-Morf). [1] A.S. Ryabova et al, Electrochimica Acta 187 (2016) 161–172. [2] A.S. Ryabova et al, ChemElectroChem 3 (2016) 1667 – 1677. [3] A.S. Ryabova et al, Electrochimica Acta 246 (2017) 643–653. [4] T. Poux et al, Catalysis Today 189 (2012) 83– 92.

Hydrogen peroxide has been identified as a stable intermediate of the electrochemical oxygen reduction reaction on various electrodes including metal, metal oxide and carbon materials. In this article we study the hydrogen peroxide oxidation and reduction reactions in alkaline medium using a rotating disc electrode (RDE) method on oxides of the perovskite family (LaCoO3, LaMnO3 and La0.8Sr0.2MnO3) which are considered as promising electrocatalytic materials for the cathode of liquid and solid alkaline fuel cells. The experimental findings, such as the higher activity of Mn-compared to that of Co-perovskites, the shape of RDE curves, and the influence of the H2O2 concentration, are rationalized with the help of a microkinetic model.

Motivation: Systems biology deals with many different types of experimental data representing individual components of biological systems. Behavior of these systems over time could be described using systems of ordinary differential equations (ODE). In order to analyze dynamics of the ODEs and estimate their parameters based on data obtained in different experimental conditions, biologists need a flexible framework that allows them to create dynamic models and perform multi-experiment parameter fitting. Results: We present optimization tools of the BioUML software ( http://biouml.org ) developed for modeling and analysis of biochemical systems. We created optimization plug-in to solve non-linear optimization problems via minimization of the function of deviations between experimental data and model simulation results. Experimental data can be considered as separate sets of time courses or steady states stored in different tab-separated files. BioUML includes several deterministic and stochastic optimization methods which find reasonably accurate solutions faster than the COPASI software. Some of these methods provide constrained optimization and some of them were parallelized.