scholarly journals OCSANA+: Optimal Control and Simulation of Signaling Networks from Network Analysis

2019 ◽  
Author(s):  
Lauren Marazzi ◽  
Andrew Gainer-Dewar ◽  
Paola Vera-Licona
Keyword(s):  
Network Analysis ◽  
Large Scale ◽  
Software Tool ◽  
Control Algorithms ◽  
Signaling Networks ◽  
Analysis Software ◽  
Link Type ◽  
Non Linear Systems ◽  
Long Term Behavior

AbstractSummaryOCSANA+ is a Cytoscape app for identifying nodes to drive the system towards a desired long-term behavior, prioritizing combinations of interventions in large scale complex networks, and estimating the effects of node perturbations in signaling networks, all based on the analysis of the network’s structure. OCSANA+ includes an update to OCSANA (optimal combinations of interventions from network analysis) software tool with cutting-edge and rigorously tested algorithms, together with recently-developed structure-based control algorithms for non-linear systems and an algorithm for estimating signal flow. All these algorithms are based on the network’s topology. OCSANA+ is implemented as a Cytoscape app to enable a user interface for running analyses and visualizing results.Availability and ImplementationOCSANA+ app and its tutorial can be downloaded from the Cytoscape App Store or https://veraliconaresearchgroup.github.io/OCSANA-Plus/. The source code and computations are available in https://github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode.

scholarly journals OCSANA+: optimal control and simulation of signaling networks from network analysis

2020 ◽  
Vol 36 (19) ◽  
pp. 4960-4962
Author(s):  
Lauren Marazzi ◽  
Andrew Gainer-Dewar ◽  
Paola Vera-Licona
Keyword(s):  
Network Analysis ◽  
Large Scale ◽  
Software Tool ◽  
Supplementary Information ◽  
Control Algorithms ◽  
Signaling Networks ◽  
Analysis Software ◽  
Non Linear Systems ◽  
Long Term Behavior

Abstract Summary OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, prioritizing combinations of interventions in large-scale complex networks, and estimating the effects of node perturbations in signaling networks, all based on the analysis of the network’s structure. OCSANA+ includes an update to optimal combinations of interventions from network analysis software tool with cutting-edge and rigorously tested algorithms, together with recently developed structure-based control algorithms for non-linear systems and an algorithm for estimating signal flow. All these algorithms are based on the network’s topology. OCSANA+ is implemented as a Cytoscape app to enable a user interface for running analyses and visualizing results. Availability and implementation OCSANA+ app and its tutorial can be downloaded from the Cytoscape App Store or https://veraliconaresearchgroup.github.io/OCSANA-Plus/. The source code and computations are available in https://github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Lost in migration: document quality for batch conversion to PDF/A

2018 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Roland Erwin Suri ◽  
Mohamed El-Saad
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Batch Processing ◽  
Digital Archives ◽  
Adobe Acrobat ◽  
Content Type ◽  
Text Document ◽  
File Formats ◽  
Long Term Preservation

PurposeChanges in file format specifications challenge long-term preservation of digital documents. Digital archives thus often focus on specific file formats that are well suited for long-term preservation, such as the PDF/A format. Since only few customers submit PDF/A files, digital archives may consider converting submitted files to the PDF/A format. The paper aims to discuss these issues.Design/methodology/approachThe authors evaluated three software tools for batch conversion of common file formats to PDF/A-1b: LuraTech PDF Compressor, Adobe Acrobat XI Pro and 3-HeightsTMDocument Converter by PDF Tools. The test set consisted of 80 files, with 10 files each of the eight file types JPEG, MS PowerPoint, PDF, PNG, MS Word, MS Excel, MSG and “web page.”FindingsBatch processing was sometimes hindered by stops that required manual interference. Depending on the software tool, three to four of these stops occurred during batch processing of the 80 test files. Furthermore, the conversion tools sometimes failed to produce output files even for supported file formats: three (Adobe Pro) up to seven (LuraTech and 3-HeightsTM) PDF/A-1b files were not produced. Since Adobe Pro does not convert e-mails, a total of 213 PDF/A-1b files were produced. The faithfulness of each conversion was investigated by comparing the visual appearance of the input document with that of the produced PDF/A-1b document on a computer screen. Meticulous visual inspection revealed that the conversion to PDF/A-1b impaired the information content in 24 of the converted 213 files (11 percent). These reproducibility errors included loss of links, loss of other document content (unreadable characters, missing text, document part missing), updated fields (reflecting time and folder of conversion), vector graphics issues and spelling errors.Originality/valueThese results indicate that large-scale batch conversions of heterogeneous files to PDF/A-1b cause complex issues that need to be addressed for each individual file. Even with considerable efforts, some information loss seems unavoidable if large numbers of files from heterogeneous sources are migrated to the PDF/A-1b format.

Natural Analogues: Their Application to the Prediction of the Long-Term Behavior of Nuclear Waste Forms

1986 ◽  
Vol 84 ◽  
Author(s):  
Rodney C. Ewing ◽  
Michael J. Jercinovic
Keyword(s):  
Nuclear Waste ◽  
Borosilicate Glass ◽  
Large Scale ◽  
Laboratory Data ◽  
Waste Form ◽  
Long Time ◽  
Natural Analogues ◽  
Long Term Behavior ◽  
Nuclear Waste Forms

AbstractOne of the unique and scientifically most difficult aspects of nuclear waste isolation is the extrapolation ofshot-term laboratory data (hours to years) to the long time periods (103-105 years) required by regulatory agencies for performance assessment. The direct verification of these extrapolations is not possible, but methods must be developed to demonstrate compliance with government regulations and to satisfy the lay public that there is a demonstrable and reasonable basis for accepting the long-term extrapolations. Natural analogues of both the repository environment (e.g. radionuclide migration at Oklo) and nuclear waste form behavior (e.g. alteration of basaltic glasses and radiation damage in minerals) have been used to demonstrate the long-term behavior of large scale geologic systems and, on a smaller scale, waste form durability. This paper reviews the use of natural analogues to predict the long-term behavior of nuclear waste form glasses. Particular emphasis is placed on the inherent limitations of any conclusions that are based on “proof” by analogy. An example -- corrosion of borosilicate glass -- is discussed in detail with specific attention to the proper and successful use of natural analogues (basaltic glass) in understanding the long-term corrosion behavior of borosilicate glass.

Sizing and Scaling Requirements of a Large-Scale Physical Model for Code Validation

1989 ◽  
Vol 176 ◽  
Author(s):  
R. Khaleel ◽  
T. Legore
Keyword(s):  
Numerical Simulation ◽  
Physical Model ◽  
Large Scale ◽  
Porous Media Flow ◽  
Isolation System ◽  
The Media ◽  
Simulation Results ◽  
Long Term Behavior ◽  
Porous Medium Model

ABSTRACTScaling considerations relevant to porous media flow are reviewed. An analysis approach is presented for determining the sizing requirements of a large-scale, hydrology physical model. The physical model will be used to validate performance assessment codes that evaluate the long-term behavior of the repository isolation system. Numerical simulation results for sizing requirements are presented for a porous medium model in which the media properties are spatially uncorrelated.

scholarly journals Long-term Behavior of CO2 Stored on a Large Scale in the Utsira Formation, the North Sea, Norwegian Continental Shelf

2013 ◽  
Vol 37 ◽  
pp. 5240-5247
Author(s):  
V.T.H. Pham ◽  
E.K. Halland ◽  
I.M. Tappel ◽  
I.T. Gjeldvik ◽  
F. Riis ◽  
...  
Keyword(s):  
Continental Shelf ◽  
North Sea ◽  
Large Scale ◽  
The North ◽  
The North Sea ◽  
Long Term Behavior ◽  
Norwegian Continental Shelf

DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS

2005 ◽  
Vol 03 (02) ◽  
pp. 415-436 ◽  
Author(s):  
STEPHEN RAMSEY ◽  
DAVID ORRELL ◽  
HAMID BOLOURI
Keyword(s):  
Regulatory Networks ◽  
Large Scale ◽  
Software Tool ◽  
Genetic Regulatory Networks ◽  
Signaling Networks ◽  
Simulation Framework ◽  
Kinetic Rate ◽  
Rate Laws ◽  
Reaction Processes ◽  
Kinetics Of

We describe Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks. Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization.

scholarly journals Pumping of Rossby Waves and Vortices at the Base of the Solar Convection Zone

1998 ◽  
Vol 185 ◽  
pp. 177-178
Author(s):  
Evgeniy Tikhomolov
Keyword(s):  
Large Scale ◽  
Rossby Waves ◽  
Convection Zone ◽  
Polar Field ◽  
Field Reversal ◽  
Solar Convection Zone ◽  
Magnetic Structures ◽  
Solar Convection ◽  
Long Term Behavior

Rossby vortices excited near the base of the solar convection zone are very appealing objects for interpretation of a number of solar phenomena such as long-lived large-scale magnetic structures, the poleward drift of the axisymmetric components after the polar field reversal, and a peculiar long-term behavior of the nonaxisymmetric components (Tikhomolov and Mordvinov 1996).

scholarly journals Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Oliver Schwengers ◽  
Patrick Barth ◽  
Linda Falgenhauer ◽  
Torsten Hain ◽  
Trinad Chakraborty ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Software Tool ◽  
High Sensitivity ◽  
Independent Manner ◽  
Short Read ◽  
Content Type ◽  
Link Type ◽  
Antimicrobial Resistance Genes

Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in the environmental adaptation of bacteria. Due to potential mobilization or conjugation capabilities, plasmids are important genetic vehicles for antimicrobial resistance genes and virulence factors with huge and increasing clinical implications. They are therefore subject to large genomic studies within the scientific community worldwide. As a result of rapidly improving next-generation sequencing methods, the quantity of sequenced bacterial genomes is constantly increasing, in turn raising the need for specialized tools to (i) extract plasmid sequences from draft assemblies, (ii) derive their origin and distribution, and (iii) further investigate their genetic repertoire. Recently, several bioinformatic methods and tools have emerged to tackle this issue; however, a combination of high sensitivity and specificity in plasmid sequence identification is rarely achieved in a taxon-independent manner. In addition, many software tools are not appropriate for large high-throughput analyses or cannot be included in existing software pipelines due to their technical design or software implementation. In this study, we investigated differences in the replicon distributions of protein-coding genes on a large scale as a new approach to distinguish plasmid-borne from chromosome-borne contigs. We defined and computed statistical discrimination thresholds for a new metric: the replicon distribution score (RDS), which achieved an accuracy of 96.6 %. The final performance was further improved by the combination of the RDS metric with heuristics exploiting several plasmid-specific higher-level contig characterizations. We implemented this workflow in a new high-throughput taxon-independent bioinformatics software tool called Platon for the recruitment and characterization of plasmid-borne contigs from short-read draft assemblies. Compared to PlasFlow, Platon achieved a higher accuracy (97.5 %) and more balanced predictions (F1=82.6 %) tested on a broad range of bacterial taxa and better or equal performance against the targeted tools PlasmidFinder and PlaScope on sequenced Escherichia coli isolates. Platon is available at: http://platon.computational.bio/.

Evolution of Large-Scale Coronal Structures

1994 ◽  
Vol 144 ◽  
pp. 29-33
Author(s):  
P. Ambrož
Keyword(s):  
Magnetic Field ◽  
Field Line ◽  
Large Scale ◽  
Coronal Magnetic Field ◽  
Source Surface ◽  
Solar Cycles ◽  
Characteristic Relationship ◽  
The Magnetic Field ◽  
Coronal Structures

AbstractThe large-scale coronal structures observed during the sporadically visible solar eclipses were compared with the numerically extrapolated field-line structures of coronal magnetic field. A characteristic relationship between the observed structures of coronal plasma and the magnetic field line configurations was determined. The long-term evolution of large scale coronal structures inferred from photospheric magnetic observations in the course of 11- and 22-year solar cycles is described.Some known parameters, such as the source surface radius, or coronal rotation rate are discussed and actually interpreted. A relation between the large-scale photospheric magnetic field evolution and the coronal structure rearrangement is demonstrated.

Sign in / Sign up

Export Citation Format

Share Document