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 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 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.

SW-Tandem: a highly efficient tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight

2019 ◽  
Vol 35 (19) ◽  
pp. 3861-3863 ◽  
Author(s):  
Chuang Li ◽  
Kenli Li ◽  
Tao Chen ◽  
Yunping Zhu ◽  
Qiang He
Keyword(s):  
Large Scale ◽  
Peptide Identification ◽  
Software Tool ◽  
Critical Issue ◽  
Peptide Sequencing ◽  
Peptide Sequence ◽  
Supplementary Information ◽  
Database Searching ◽  
Sunway Taihulight ◽  
Dot Product

Abstract Summary Tandem mass spectrometry based database searching is a widely acknowledged and adopted method that identifies peptide sequence in shotgun proteomics. However, database searching is extremely computationally expensive, which can take days even weeks to process a large spectra dataset. To address this critical issue, this paper presents SW-Tandem, a new tool for large-scale peptide sequencing. SW-Tandem parallelizes the spectrum dot product scoring algorithm and leverages the advantages of Sunway TaihuLight, the No. 1 supercomputer in the world in 2017. Sunway TaihuLight is powered by the brand new many-core SW26010 processors and provides a peak computation performance greater than 100PFlops. To fully utilize the Sunway TaihuLights capacity, SW-Tandem employs three mechanisms to accelerate large-scale peptide identification, memory-access optimizations, double buffering and vectorization. The results of experiments conducted on multiple datasets demonstrate the performance of SW-Tandem against three state-of-the-art tools for peptide identification, including X!! Tandem, MR-Tandem and MSFragger. In addition, it shows high scalability in the experiments on extremely large datasets sized up to 12 GB. Availability and implementation SW-Tandem is an open source software tool implemented in C++. The source code and the parameter settings are available at https://github.com/Logic09/SW-Tandem. Supplementary information Supplementary data are available at Bioinformatics online.

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 Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection

2020 ◽  
Vol 36 (9) ◽  
pp. 2862-2871
Author(s):  
Chiung-Ting Wu ◽  
Yizhi Wang ◽  
Yinxue Wang ◽  
Timothy Ebbels ◽  
Ibrahim Karaman ◽  
...  
Keyword(s):  
Large Scale ◽  
Synthetic Data ◽  
Software Tool ◽  
R Package ◽  
Supplementary Information ◽  
Internal Quality ◽  
Systematic Change ◽  
Warping Function ◽  
Time Warping ◽  
Alignment Algorithms

Abstract Motivation Liquid chromatography–mass spectrometry (LC-MS) is a standard method for proteomics and metabolomics analysis of biological samples. Unfortunately, it suffers from various changes in the retention times (RT) of the same compound in different samples, and these must be subsequently corrected (aligned) during data processing. Classic alignment methods such as in the popular XCMS package often assume a single time-warping function for each sample. Thus, the potentially varying RT drift for compounds with different masses in a sample is neglected in these methods. Moreover, the systematic change in RT drift across run order is often not considered by alignment algorithms. Therefore, these methods cannot effectively correct all misalignments. For a large-scale experiment involving many samples, the existence of misalignment becomes inevitable and concerning. Results Here, we describe an integrated reference-free profile alignment method, neighbor-wise compound-specific Graphical Time Warping (ncGTW), that can detect misaligned features and align profiles by leveraging expected RT drift structures and compound-specific warping functions. Specifically, ncGTW uses individualized warping functions for different compounds and assigns constraint edges on warping functions of neighboring samples. Validated with both realistic synthetic data and internal quality control samples, ncGTW applied to two large-scale metabolomics LC-MS datasets identifies many misaligned features and successfully realigns them. These features would otherwise be discarded or uncorrected using existing methods. The ncGTW software tool is developed currently as a plug-in to detect and realign misaligned features present in standard XCMS output. Availability and implementation An R package of ncGTW is freely available at Bioconductor and https://github.com/ChiungTingWu/ncGTW. A detailed user’s manual and a vignette are provided within the package. Supplementary information Supplementary data are available at Bioinformatics online.

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).

Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis

2019 ◽  
Vol 35 (22) ◽  
pp. 4739-4747 ◽  
Author(s):  
Longendri Aguilera-Mendoza ◽  
Yovani Marrero-Ponce ◽  
Jesus A Beltran ◽  
Roberto Tellez Ibarra ◽  
Hugo A Guillen-Ramirez ◽  
...  
Keyword(s):  
Network Analysis ◽  
Data Entry ◽  
Software Tool ◽  
Bioactive Peptide ◽  
Supplementary Information ◽  
Web Pages ◽  
Web Content ◽  
Unified View ◽  
User Friendly ◽  
Visual Network

Abstract Motivation Bioactive peptides have gained great attention in the academy and pharmaceutical industry since they play an important role in human health. However, the increasing number of bioactive peptide databases is causing the problem of data redundancy and duplicated efforts. Even worse is the fact that the available data is non-standardized and often dirty with data entry errors. Therefore, there is a need for a unified view that enables a more comprehensive analysis of the information on this topic residing at different sites. Results After collecting web pages from a large variety of bioactive peptide databases, we organized the web content into an integrated graph database (starPepDB) that holds a total of 71 310 nodes and 348 505 relationships. In this graph structure, there are 45 120 nodes representing peptides, and the rest of the nodes are connected to peptides for describing metadata. Additionally, to facilitate a better understanding of the integrated data, a software tool (starPep toolbox) has been developed for supporting visual network analysis in a user-friendly way; providing several functionalities such as peptide retrieval and filtering, network construction and visualization, interactive exploration and exporting data options. Availability and implementation Both starPepDB and starPep toolbox are freely available at http://mobiosd-hub.com/starpep/. Supplementary information Supplementary data are available at Bioinformatics online.

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