scholarly journals AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context

2009 ◽  
Vol 25 (5) ◽  
pp. 662-663 ◽  
Author(s):  
Olivier Martin ◽  
Armand Valsesia ◽  
Amalio Telenti ◽  
Ioannis Xenarios ◽  
Brian J. Stevenson
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Genomic Context ◽  
Variation Data ◽  
Integrated Software ◽  
Scale Variation

scholarly journals CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

scholarly journals pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation

2021 ◽  
Author(s):  
Weiqian Cao ◽  
Siyuan Kong ◽  
Wenfeng Zeng ◽  
Pengyun Gong ◽  
Biyun Jiang ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Large Scale ◽  
Missing Values ◽  
Software Tool ◽  
Software Tools ◽  
Residual Network ◽  
Site Specific ◽  
Carcinoma Cell Lines ◽  
L1 Cell Adhesion Molecule

Interpreting large-scale glycoproteomic data for intact glycopeptide identification has been tremendously advanced by software tools. However, software tools for quantitative analysis of intact glycopeptides remain lagging behind, which greatly hinders exploring the differential expression and functions of site-specific glycosylation in organisms. Here, we report pGlycoQuant, a generic software tool for accurate and convenient quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant enables intact glycopeptide quantitation with very low missing values via a deep residual network, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco. The pGlycoQuant-based site-specific N-glycoproteomic study conducted here quantifies 6435 intact N-glycopeptides in three hepatocellular carcinoma cell lines with different metastatic potentials and, together with in vitro molecular biology experiments, illustrates core fucosylation at site 979 of the L1 cell adhesion molecule (L1CAM) as a potential regulator of HCC metastasis. pGlycoQuant is freely available at https://github.com/expellir-arma/pGlycoQuant/releases/. We have demonstrated pGlycoQuant to be a powerful tool for the quantitative analysis of site-specific glycosylation and the exploration of potential glycosylation-related biomarker candidates, and we expect further applications in glycoproteomic studies.

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.

scholarly journals Author Correction: Large-scale variation in density of an aquatic ecosystem indicator species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chris Sutherland ◽  
Angela K. Fuller ◽  
J. Andrew Royle ◽  
Matthew P. Hare ◽  
Sean Madden
Keyword(s):  
Indicator Species ◽  
Aquatic Ecosystem ◽  
Large Scale ◽  
Scale Variation

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Demand Response Model Development for Smart Households Using Time of Use Tariffs and Optimal Control—The Isle of Wight Energy Autonomous Community Case Study

Energies ◽  
2020 ◽  
Vol 13 (3) ◽  
pp. 541 ◽  
Author(s):  
Sourav Khanna ◽  
Victor Becerra ◽  
Adib Allahham ◽  
Damian Giaouris ◽  
Jamie M. Foster ◽  
...  
Keyword(s):  
Demand Response ◽  
Large Scale ◽  
Energy Transport ◽  
Model Development ◽  
Software Tool ◽  
Load Flow ◽  
Smart Devices ◽  
Smart Meters ◽  
Isle Of Wight

Residential variable energy price schemes can be made more effective with the use of a demand response (DR) strategy along with smart appliances. Using DR, the electricity bill of participating customers/households can be minimised, while pursuing other aims such as demand-shifting and maximising consumption of locally generated renewable-electricity. In this article, a two-stage optimization method is used to implement a price-based implicit DR scheme. The model considers a range of novel smart devices/technologies/schemes, connected to smart-meters and a local DR-Controller. A case study with various decarbonisation scenarios is used to analyse the effects of deploying the proposed DR-scheme in households located in the west area of the Isle of Wight (Southern United Kingdom). There are approximately 15,000 households, of which 3000 are not connected to the gas-network. Using a distribution network model along with a load flow software-tool, the secondary voltages and apparent-power through transformers at the relevant substations are computed. The results show that in summer, participating households could export up to 6.4 MW of power, which is 10% of installed large-scale photovoltaics (PV) capacity on the island. Average carbon dioxide equivalent (CO2e) reductions of 7.1 ktons/annum and a reduction in combined energy/transport fuel-bills of 60%/annum could be achieved by participating households.

An Integrated Software Tool for High Fidelity Probabilistic Assessments of Metallic Aero-Engine Components

2016 ◽  
Author(s):  
R. Craig McClung ◽  
Paul Wawrzynek ◽  
Yi-Der Lee ◽  
Bruce J. Carter ◽  
Jonathan P. Moody ◽  
...  
Keyword(s):  
Crack Growth ◽  
Degrees Of Freedom ◽  
Software Tool ◽  
High Fidelity ◽  
Fatigue Lifetime ◽  
Turbine Engine ◽  
Engine Components ◽  
Integrated Software ◽  
Combined Work ◽  
Exchange Data

Most current tools and methodologies to predict the life and reliability of fracture critical gas turbine engine components rely on stress intensity factor solutions that assume highly idealized component and crack geometries, and this can lead to highly conservative results in some cases. This paper describes a new integrated methodology to perform these assessments that combines one software tool for creating high fidelity crack growth simulations (FRANC3D) with another software tool for performing probabilistic fatigue crack growth life assessments of turbine engine components (DARWIN). DARWIN employs finite element models of component stresses, while FRANC3D performs automatic adaptive re-meshing of these models to simulate crack growth. Modifications have been performed to both codes to allow them to share and exchange data and to enhance their shared computational capabilities. Most notably, a new methodology was developed to predict the shape evolution and the fatigue lifetime for cracks that are geometrically complex and not easily parameterized by a small number of degrees of freedom. This paper describes the integrated software system and the typical combined work flow, and it shows the results from a number of analyses that demonstrate the significant features of the system.

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