1,721,031 research outputs found
A Formal Approach to Molecular Docking
No full textDrugs are small molecules designed to regulate the activity of specific biological receptors. Design new drugs is long and expensive, because modifying the behavior of a receptor may have unpredicted side effects. Two paradigms aim to speed up the drug discovery process: molecular docking estimates if two molecules can bind, to predict unwanted interactions; systems biology studies the effects of pharmacological intervention from a system perspective, to identify pathways related to the disease. In this paper we start from process calculi theory to integrate information from molecular docking into systems biology paradigm. In particular, we introduce Beta-binders, a process calculus for representing molecular complexation driven by the shape of the ligands involved and the subsequent molecular changes
GPU computing for systems biology
No full textThe development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological systems. However, the computational power required by these simulations often exceeds that available on common desktop computers and thus expensive high performance computing solutions are required. An emerging alternative is represented by general-purpose scientific computing on graphics processing units (GPGPU), which offers the power of a small computer cluster at a cost of ∼$400. Computing with a GPU requires the development of specific algorithms, since the programming paradigm substantially differs from traditional CPU-based computing. In this paper, we review some recent efforts in exploiting the processing power of GPUs for the simulation of biological systems
Stability Analysis of Biological Network Topologies during Stochastic Simulation
No full textRecent advances in the stochastic simulation of biological systems have exploited the weighted dependency di-graph as a compact representation of the computational workload. It was largely used to represent the causal relationships among reactions and then to determine their cause-eect implica- tions. Although critical for several applications, the topol- ogy of the dependency graph has been little studied so far. Here, we make use of some network topology indices to de- tect and characterize the important reactions of two real case studies. We measure the stability of such indices over time and make a case for considering them in parallel stochastic simulation
Ploidy‐ and Purity‐Adjusted Allele‐Specific DNA Analysis Using CLONETv2
No full text: High-throughput DNA sequencing technology provides base-level and statistically rich information about the genomic content of a sample. In the contexts of cancer research and precision oncology, thousands of genomes from paired tumor and matched normal samples are profiled and processed to determine somatic copy-number changes and single-nucleotide variations. Higher-order informative analyses, in the form of allele-specific copy-number assessments or subclonality quantification, require reliable estimates of tumor DNA ploidy and tumor cellularity. CLONETv2 provides a complete set of functions to process matched normal and tumor pairs using patient-specific genotype data, is independent of low-level tools (e.g., aligner, segmentation algorithm, mutation caller) and offers high-level functions to compute allele-specific copy number from segmented data and to identify subclonal population in the input sample. CLONETv2 is applicable to whole-genome, whole-exome and targeted sequencing data generated either from tissue or from liquid biopsy samples. © 2019 The Authors
Stochastic COWS
No full textA stochastic extension of COWS is presented. First the formalism is given an operational semantics leading to finitely branching transition systems. Then its syntax and semantics are enriched along the lines of Markovian extensions of process calculi. This allows addressing quantitative reasoning about the behaviour of the specified web services. For instance, a simple case study shows that services can be analyzed using the PRISM probabilistic model checker
Formal analysis of BPMN via a translation into COWS
No full textA translation of the Business Process Modeling Notation into the process calculus COWS is presented. The stochastic extension of COWS is then exploited to address quantitative reasoning about the behaviour of business processes. An example of such reasoning is shown by running the PRISM probabilistic model checker on a case study
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
On the regularity of abnormal minimizers for rank 2 sub-Riemannian structures
No full textWe prove the C1 regularity for a class of abnormal length-minimizers in rank 2 sub-Riemannian structures. As a consequence of our result, all length-minimizers for rank 2 sub-Riemannian structures of step up to 4 are of class C1
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